SELENOPROTEÍNAS DE Meleagris Gallopavo
PROTEIN REPORT FOR Selenoprotein N (SelN)
| DESCRIPCIÓN | Selenoproteína. 25(-):2019159...2009276. |
| SECISearch | Un elemento predicho en la cadena antisense. 25:subseq(2009159,10000):[4580,4471] |
| SELENOPROFILES | Encontrada. Elección: Genewise. Elemento SECIS predicho (chromosome:25 strand:- positions:2006676-2006771) |
| COMENTARIOS | Elección: Genewise. Nuestra predicción concuerda con la de selenoprofiles. La primera selenocisteína no está presente en nuestras predicciones ya que queda alineada con una región con muchos gaps. De hecho, solo está presente en SPP00000018_1.0 (Sel N de Homo sapiens. Nuestra predicción se alinea mejor con la Sel N de Mus musculus, que no tiene este fragmento de exón. Este caso es interesante y merecería un estudio en más profundidad ya que podría haberse dado el caso de que en humano se haya exonizado un fragmento que ha aportado una selenocisteína de más. |
1. ALINEAMIENTO MÚLTIPLE DE TODOS LOS HOMÓLOGOS DE SELENODB
2. BEST PAIRWISE ALIGNMENT
3. RESULTADOS DEL SECISearch
4. RESULTADOS DEL Selenoprofiles
ALINEAMIENTO MÚLTIPLE DE TODOS LOS HOMÓLOGOS DE SELENODB
CLUSTAL FORMAT for T-COFFEE Version_7.54, CPU=3.20 sec, SCORE=97, Nseq=6, Len=600
SPP00000018_1.0 MGRARPGQRGPPSPGPAAQPPAPPRRRARSLALLGALLAAAAA-AAVRVCARHAEAQAAA
SPP00000018_1.0.25.exonerate A----------------VHPAADNREGRRTLPFLTKLCRAHQ-NTALNLPEQ-RKCRTAQ
SPP00000018_1.0.25.genewise ------------------------------------------------------------
SPP00000114_1.0 MGQARPAARRPHSPDPGAQP-APPRRRARALALLGALLAAAAAVAAARACALLADAQAAA
SPP00000114_1.0.25.exonerate V--------------------------------RSAFVRGRAPRAAPCCCAL-PGCALAT
SPP00000114_1.0.25.genewise ------------------------------------------------------------
SPP00000018_1.0 RQEL-----ALKTLGTDGLFLFSSLDTDGDMYISPEEFKPIAEKLTGSCSVTQT--GVQW
SPP00000018_1.0.25.exonerate REEQ-----ALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTGSFQLSLH--RLRQ
SPP00000018_1.0.25.genewise ---x-----ALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTGSFQLSLHXTEQKQ
SPP00000114_1.0 RQES-----ALKVLGTDGLFLFSSLDTDQDMYISPEEFKPIAEKLTGS------------
SPP00000114_1.0.25.exonerate LNCLALSXXALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTG-------------
SPP00000114_1.0.25.genewise ---------ALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTG-------------
*** **::**********: *:*:**************
SPP00000018_1.0 CSHSSLQPQLPWLNUSSCLSLLRSTPAASCEEEELPPDPSEETLTIEARFQPLLPETMTK
SPP00000018_1.0.25.exonerate CSDSWEAPSAPKLV-RKNVSLYRVTPVSDFEED--VPDPNGETLSIVAKFQPLVMETMTK
SPP00000018_1.0.25.genewise FLLM-------SL--FFLGAVLGVTPVSDFEED--VPDPNGETLSIVAKFQPLVMETMTK
SPP00000114_1.0 ------------------------VPVANYEEEELPHDPSEETLTIEARFQPLLMETMTK
SPP00000114_1.0.25.exonerate -----------------------VTPVSDFEED--VPDPNGETLSIVAKFQPLVMETMTK
SPP00000114_1.0.25.genewise -----------------------VTPVSDFEED--VPDPNGETLSIVAKFQPLVMETMTK
.*.:. **: **. ***:* *:****: *****
SPP00000018_1.0 SKDGFLGVSRLALSGLRNWTAAASPSAVFATRHFQPFLPPPGQ-ELGEPWWIIPSELSMF
SPP00000018_1.0.25.exonerate SKDGFLGISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKNKLDLGDPWWIIPSELNIF
SPP00000018_1.0.25.genewise SKDGFLGISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKNKLDLGDPWWIIPSELNIF
SPP00000114_1.0 SKDGFLGVSRLALSGLRNWTTAASPSAAFAARHFRPFLPPPGQ-ELGQPWWIIPGELSVF
SPP00000114_1.0.25.exonerate SKDGFLGISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKNKLDLGDPWWIIPSELNIF
SPP00000114_1.0.25.genewise SKDGFLGISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKNKLDLGDPWWIIPSELNIF
*******:*::*********:..**.:.: :*:*:.**** .: :**:******.**.:*
SPP00000018_1.0 TGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGAVACLTAISDFYYTVMFR
SPP00000018_1.0.25.exonerate TGYLSNNRFYPPPPKGKEIIIHRLLSMFHPRPFVKTRFAPQGSVACIQAISTYYYTIAFR
SPP00000018_1.0.25.genewise TGYLSNNRFYPPPPKGKEIIIHRLLSMFHPRPFVKTRFAPQGSVACIQAISTYYYTIAFR
SPP00000114_1.0 TGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQGTVACLTAISDSYYTVMFR
SPP00000114_1.0.25.exonerate TGYLSNNRFYPPPPKGKEIIIHRLLSMFHPRPFVKTRFAPQGSVACIQAISTYYYTIAFR
SPP00000114_1.0.25.genewise TGYLSNNRFYPPPPKGKEIIIHRLLSMFHPRPFVKTRFAPQGSVACIQAISTYYYTIAFR
******************:***********************:***: *** ***: **
SPP00000018_1.0 IHAEFQLSEPPDFPFWFSPAQFTGHIILSKDATHVRDFRLFVPNHRSLNVDMEWLYGASE
SPP00000018_1.0.25.exonerate IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFVPNKRSLNVDMEWLYGASE
SPP00000018_1.0.25.genewise IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFVPNKRSLNVDMEWLYGASE
SPP00000114_1.0 IHAEFQLSEPPDFPFWFSPGQFTGHIILSKDATHIRDFRLFVPNHRSLNVDMEWLYGASE
SPP00000114_1.0.25.exonerate IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFVPNKRSLNVDMEWLYGASE
SPP00000114_1.0.25.genewise IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFVPNKRSLNVDMEWLYGASE
*******.***********.****:*:****::*:*:*:*****:***************
SPP00000018_1.0 SSNMEVDIGYIPQMELEATGPSVPSVILDEDGSMIDSHLPSGEPLQFVFEEIKWQQELSW
SPP00000018_1.0.25.exonerate GSNMEVDIGYLPQMELESTGPSVPSVIYDENGNVIDSRDPSGEPIQFVFEEITWQQEISW
SPP00000018_1.0.25.genewise GSNMEVDIGYLPQMELESTGPSVPSVIYDENGNVIDSRDPSGEPIQFVFEEITWQQEISW
SPP00000114_1.0 TSNMEVDIGYVPQMELEAVGPSVPSVILDEDGNMIDSRLPSGEPLQFVFEEIKWHQELSW
SPP00000114_1.0.25.exonerate GSNMEVDIGYLPQMELESTGPSVPSVIYDENGNVIDSRDPSGEPIQFVFEEITWQQEISW
SPP00000114_1.0.25.genewise GSNMEVDIGYLPQMELESTGPSVPSVIYDENGNVIDSRDPSGEPIQFVFEEITWQQEISW
*********:******:.******** **:*.:***: *****:*******.*:**:**
SPP00000018_1.0 EEAARRLEVAMYPFKKVSYLPFTEAFDRAKAENKLVHSILLWGALDDQSCUGSGRTLRET
SPP00000018_1.0.25.exonerate EEAAQKLEVAMYPFKKVSYLPFTEAFERAKAEKKLVHSILLWGALDDQSCUGSGRTLRET
SPP00000018_1.0.25.genewise EEAAQKLEVAMYPFKKVSYLPFTEAFERAKAEKKLVHSILLWGALDDQSCUGSGRTLRET
SPP00000114_1.0 EEAARRLEVAMYPFKKVNYLPFTEAFDRARAEKKLVHSILLWGALDDQSCUGSGRTLRET
SPP00000114_1.0.25.exonerate EEAAQKLEVAMYPFKKVSYLPFTEAFERAKAEKKLVHSILLWGALDDQSCUGSGRTLRET
SPP00000114_1.0.25.genewise EEAAQKLEVAMYPFKKVSYLPFTEAFERAKAEKKLVHSILLWGALDDQSCUGSGRTLRET
****::***********.********:**:**:***************** *********
SPP00000018_1.0 VLESSPILTLLNESFISTWSLVKELEELQNNQENSSHQKLAGLHLEKYSFPVEMMICLPN
SPP00000018_1.0.25.exonerate VLESSPILALLNESFISSWSLVKELEELQTNRENEFYSKLADLHLEKYNFPVEMIICLPN
SPP00000018_1.0.25.genewise VLESSPILALLNESFISSWSLVKELEELQTNRENEFYSKLADLHLEKYNFPVEMIICLPN
SPP00000114_1.0 VLESPPILTLLNESFISTWSLVKELEDLQTQQENPLHRQLAGLHLEKYSFPVEMMICLPN
SPP00000114_1.0.25.exonerate VLESSPILALLNESFISSWSLVKELEELQTNRENEFYSKLADLHLEKYNFPVEMIICLPN
SPP00000114_1.0.25.genewise VLESSPILALLNESFISSWSLVKELEELQTNRENEFYSKLADLHLEKYNFPVEMIICLPN
****.***:********:********:**.::** : :**.******.*****:*****
SPP00000018_1.0 GTVVHHINANYFLDITSVKPEEIES-NLFSFSSTFEDPSTATYMQFLKEGLRRGLPLLQP
SPP00000018_1.0.25.exonerate GTVIHHINANYFLDITSMKPEDVES-SIFSFSSSFDDPSTATYLQFLKEGLQRAKAYL-Q
SPP00000018_1.0.25.genewise GTVIHHINANYFLDITSMKPEDVES-SIFSFSSSFDDPSTATYLQFLKEGLQRAKAYL-Q
SPP00000114_1.0 GTVVHHINANYFLDITSMKPEDMENNNVFSFSSSFEDPSTATYMQFLREGLRRGLPLLQP
SPP00000114_1.0.25.exonerate GTVIHHINANYFLDITSMKPEDVES-SIFSFSSSFDDPSTATYLQFLKEGLQRAKAYL-Q
SPP00000114_1.0.25.genewise GTVIHHINANYFLDITSMKPEDVES-SIFSFSSSFDDPSTATYLQFLKEGLQRAKAYL-Q
***:*************:***::*. .:*****:*:*******:***:***:*. . *
......................................................................................................................................................................................................................................................
BEST PAIRWISE ALIGNMENT
CLUSTAL FORMAT for T-COFFEE Version_7.54, SCORE=98, Nseq=2, Len=558
SPP00000114_1.0 MGQARPAARRPHSPDPGAQPAPPRRRARALALLGALLAAAAAVAAARACALLADAQAAAR
SPP00000114_1.0.25.genewise ------------------------------------------------------------
SPP00000114_1.0 QESALKVLGTDGLFLFSSLDTDQDMYISPEEFKPIAEKLTGSVPVANYEEEELPHDPSEE
SPP00000114_1.0.25.genewise ---ALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTGVTPVSDFEED-VP-DPNGE
*** **::**********::*:*:************** .**:::**: :* **. *
SPP00000114_1.0 TLTIEARFQPLLMETMTKSKDGFLGVSRLALSGLRNWTTAASPSAAFAARHFRPFLPPPG
SPP00000114_1.0.25.genewise TLSIVAKFQPLVMETMTKSKDGFLGISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKN
**:* *:****:*************:*::*********:..**.:.: **:*:.**** .
SPP00000114_1.0 Q-ELGQPWWIIPGELSVFTGYLSNNRFYPPPPKGKEVIIHRLLSMFHPRPFVKTRFAPQG
SPP00000114_1.0.25.genewise KLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKEIIIHRLLSMFHPRPFVKTRFAPQG
: :**:******.**.:*******************:***********************
SPP00000114_1.0 TVACLTAISDSYYTVMFRIHAEFQLSEPPDFPFWFSPGQFTGHIILSKDATHIRDFRLFV
SPP00000114_1.0.25.genewise SVACIQAISTYYYTIAFRIHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFV
:***: *** ***: *********.****************:*:****::*:*:*:***
SPP00000114_1.0 PNHRSLNVDMEWLYGASETSNMEVDIGYVPQMELEAVGPSVPSVILDEDGNMIDSRLPSG
SPP00000114_1.0.25.genewise PNKRSLNVDMEWLYGASEGSNMEVDIGYLPQMELESTGPSVPSVIYDENGNVIDSRDPSG
**:*************** *********:******:.******** **:**:**** ***
SPP00000114_1.0 EPLQFVFEEIKWHQELSWEEAARRLEVAMYPFKKVNYLPFTEAFDRARAEKKLVHSILLW
SPP00000114_1.0.25.genewise EPIQFVFEEITWQQEISWEEAAQKLEVAMYPFKKVSYLPFTEAFERAKAEKKLVHSILLW
**:*******.*:**:******::***********.********:**:************
SPP00000114_1.0 GALDDQSCUGSGRTLRETVLESPPILTLLNESFISTWSLVKELEDLQTQQENPLHRQLAG
SPP00000114_1.0.25.genewise GALDDQSCUGSGRTLRETVLESSPILALLNESFISSWSLVKELEELQTNRENEFYSKLAD
******** *************.***:********:********:***::** :: :**.
SPP00000114_1.0 LHLEKYSFPVEMMICLPNGTVVHHINANYFLDITSMKPEDMENNNVFSFSSSFEDPSTAT
SPP00000114_1.0.25.genewise LHLEKYNFPVEMIICLPNGTVIHHINANYFLDITSMKPEDVES-SIFSFSSSFDDPSTAT
******.*****:********:******************:*. .:*******:******
SPP00000114_1.0 YMQFLREGLRRGLPLLQP
SPP00000114_1.0.25.genewise YLQFLKEGLQRAKAYL-Q
*:***:***:*. . *
......................................................................................................................................................................................................................................................
RESULTADOS DEL SECISearch
>25:subseq(2009159,10000):[4580,4471] [4471 - 4580] (SECIS on complementary strand) - Free Energy: -20.61 UGGGUUGAAUCUUAACCUCCUGGAGUCACAUGAAUUUGUCUAUUUUUAAAGAGUUGACUGGCAGGCAGAAGGGAUGAGGGAGCCGAACGCAGGCUCUGA GCCCAGAGGGC
_[4580,4471].png)
......................................................................................................................................................................................................................................................
RESULTADOS DEL Selenoprofiles
Output_id: SelN.9.selenocysteine
---------- ---------------------
-Species Meleagris gallopavo -Taxid 9103
-Target /homes/users/U63748/gallopavo.fa
-Chromosome (-) 25
-Program genewise
-Query name gi|169234640|ref|NP_001108444.1| selenoprotein N, 1 [Gallus gallus]
-Query range 38-530 length:530 coverage: 0.93
-Profile range 75-569 length:569 coverage: 0.87 sec_position: [441]
-Average sequence identity with profile: 0.6859 (ignoring gaps: 0.7748)
-State kept
------- alignment -------
Query LALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTG <---Intron---> VTPVSDFEEDAPDPNGETLSIVAKFQPLVMETMTKSKDGFLG <-
|||||||||||||||||||||||||||||||||||||| < 771bp > |||||||||| ||||||||||||||||||||||||||||||| <
Target xALKSLGSEGLFLFSSLDTNNDLYLSPEEFKPIAEKLTG VTPVSDFEEDVPDPNGETLSIVAKFQPLVMETMTKSKDGFLG
ngcattgaggctctttcgaaagctcacggtacaggacag gacgtgtggggcgcaggattaggatcctgagaaaaaaggttg
nctactggagttttcctacaaatatgcaatactcaatc gtcctcataaatcacagactcttcatactttactcagaagttg
ggggcgctgggtctttgcacctgcccaagcggatggga attacactagtgttatggggctgtacgtgcgaggagcatccga
Query --Intron---> ISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKNKLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKE <---Intron--->
658bp > ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| < 662bp >
Target ISHVALSGLRNWTAPVSPKSVMLARQFKAFLPPKNKLDLGDPWWIIPSELNIFTGYLSNNRFYPPPPKGKE
atcggctgcaatagcgtcaagacgactagtcccaaacgcggcttaacagtaatagtctaaattccccagag
tcatctcgtgagccctccagtttcgatacttccaaatatgacggttcgatattcgatcaagtaccccagaa
ctcttttgggtgtttactgtggtcagtactttagtatttctgggatttagccctattcccgtctatcacag
Query IIIHRLLSMFHPRPFVKTRFAPQGSVACIQAISTYYYTIAFR <---Intron---> IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFV
|||||||||||||||||||||||||||||||||||||||||| < 727bp > ||||||||||||||||||||||||||||||||||||||||||
Target IIIHRLLSMFHPRPFVKTRFAPQGSVACIQAISTYYYTIAFR IHAEFQLNEPPDFPFWFSPGQFTGYIVLSKDSSHVREFKLFV
aaacaccaatcccctgaactgccgtggtacgaaatttaagta acggtccagccgtcttttcgctagtagctagttcgcgtactg
tttagttgttacgcttacgtccagctcgtactgcaaactctg tacatataaccatctgtccgatcgatttcaaccatgatattt
caccgtgcgccgccccaccttcaacgctcacccccctcaac gcttgcggcgaaccccgtcacgcatcccccgttctgagtgccc
Query PNKR <---Intron---> SLNVDMEWLYGASEGSNMEVDIGYLPQ <---Intron---> MELESTGPSVPSVIYDENGNVIDSRDPSGEPIQFVFE
|||| < 1609bp > ||||||||||||||||||||||||||| < 957bp > |||||||||||||||||||||||||||||||||||||
Target PNKR SLNVDMEWLYGASEGSNMEVDIGYLPQ MELESTGPSVPSVIYDENGNVIDSRDPSGEPIQFVFE
caaa tcaggagtctggaggaaagggagtccc agcgtagctgctgatggagagagaagctggcactgtg
caag ctatatagtagcgaggatatatgatca tataccgcctccttaaaagattaggaccgactattta
tcg gtgtttggggtagtacccgagtatcgtg gggacagcacctgcttgtatgtccgtcaggatgtcta
Query EITWQQEIPWEEAAQKLEVAMYPFKK <---Intron---> VSYLPFTEAFERAKAEKKLVHSILLWGALDDQSCUG <---Intron---> SGRTLR
|||||||| ||||||||||||||||| < 955bp > |||||||||||||||||||||||||||||||||||| < 854bp > ||||||
Target EITWQQEISWEEAAQKLEVAMYPFKK VSYLPFTEAFERAKAEKKLVHSILLWGALDDQSCUG SGRTLR
gaatccgattggggcacgggatctaa gttcctaggtgagaggaacgctacctggcggctttg tgcacc
atcgaaatcgaaccaatatctactaa tcatctcactagcacaaattactttggctaaacgg gcggctg
gacgggaccgagacgggagcgtatgg ccttccaattgaaaaaggggcacgggtcgtcgcca tggatcg
*
Query ETVLESSPILALLNESFISSWSLVKELEELQ <---Intron---> TNRENEFYSKLADLHLEKYNFPVEMIICLPNGTV <---Intron---> IHH
||||||||||||||||||||||||||||||| < 691bp > |||||||||||||||||||||||||||||||||| < 572bp > |||
Target ETVLESSPILALLNESFISSWSLVKELEELQ TNRENEFYSKLADLHLEKYNFPVEMIICLPNGTV IHH
gagcgatcacgccagataaattcgagcggcc aaagagttaacggcccgatatcggaaatccagag acc
acttagccttcttaagttgggcttaataata cagaaatagatcatataaaatctatttgtcagct taa
gtcgatgccccggtgcctccgatggggaggg acggtgcccggtcgctaaccctgggccctctcgg tct
Query INANYFLDITSMKPEDVESSIFSFSANFDDPSTATYLQFLKEGLQRAKAYLQN
|||||||||||||||||||||||||//||||||||||||||||||||||||||
Target INANYFLDITSMKPEDVESSIFSFSSSFDDPSTATYLQFLKEGLQRAKAYLQN
aagattcgaataacggggaaatatttatggctagatcctcaggccagagttca
tacaattatcctacaataggttgtccgtaacccccatattaagtagcacataa
ctccccgttttggtattattcttcactttctttatccgttgaagaaaatcggc
------- positions -------
Exon 1 2019054 2019168
Exon 2 2018155 2018282
Exon 3 2017284 2017496
Exon 4 2016497 2016621
Exon 5 2015632 2015769
Exon 6 2013941 2014022
Exon 7 2012795 2012983
Exon 8 2011734 2011839
Exon 9 2010767 2010879
Exon 10 2009974 2010075
Exon 11 2009234 2009401
--------- SECIS ---------
>SelN.9.selenocysteine.esecis:def.1 chromosome:25 strand:- positions:2006676-2006771 species:"Meleagris gallopavo"
target:/homes/users/U63748/gallopavo.fa distance_from_sec_uga:2846 distance_from_cds:2462
GCUGCUUUUC ACGAUCUC CUGUGCUUC GUGAC GCUCUGGCCUU AA AUCCACAA ACGGGUCAGAGC CGAU GUCUGCCAG CAGCAUUU CGUGGGAAAG
.....((((( ((((.((. (((.((... .(((( ((((((((((. .. ........ ..)))))))))) )))) ....))))) .))....) ))))))))..
--------- 3' seq --------
Total sequence length available downstream >= 3000
Sequence until first stop codon:
TAA
*
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