SELENOPROTEÍNAS DE Meleagris gallopavo
PROTEIN REPORT FOR Selenoprotein M (SelM)
| DESCRIPCIÓN | Región que ha perdido la selenocisteína. Región: 17(-):10566329...10566038 | |
| SECISearch | Elemento predicho en la cadena complementaria. 17:subseq(10556329,10000):[9245,9148] | |
| SELENOPROFILES | Encontrada. Elección: Genewise. Predicción elemento SeCis (strand:- positions:10565476-10565575) | |
| COMENTARIOS | Elección: El alineamiento de las predicciones de Exonerate y Genewise obtuvieron el mismo score pero por defecto reportamos el alineamiento de Genewise. Vemos que la primera parte de la proteína, que es la que contiene la selenocisteína, se ha perdido. El resto de la proteína sigue intacta. Esta región de la secuencia sí se encuentra en dos homólogos con selenocisteína de Homo sapiens y Mus musculus. Selenoprofiles tampoco predice la selenocisteína, pero sí hay predicción de elementos SECIS tanto en SECISearch como en Selenoprofiles. No podemos confirmar que se trate de la Sel M. |
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, SCORE=99, Nseq=6, Len=145
SPP00000017_1.0 MSLLLPPLALLLLLAALVAPATAATAYRPDWNRLSGLTRARVETCGGUQLNRLKEVKAFV
SPP00000017_1.0.17.exonerate ------------------------------------------------------------
SPP00000017_1.0.17.genewise ------------------------------------------------------------
SPP00000113_1.0 MSILLSPPSLLLLLAALVAPATSTTNYRPDWNRLRGLARGRVETCGGUQLNRLKEVKAFV
SPP00000113_1.0.17.exonerate ------------------------------------------------------------
SPP00000113_1.0.17.genewise ------------------------------------------------------------
SPP00000017_1.0 TQDIPFYHNLVMKHLPGADPELVLLGRRYEELERIPLSEMTREEINALVQELGFYRKAAP
SPP00000017_1.0.17.exonerate -------HNLEMKHLPGADPELVLLSFRYEELERIPLSDMTREEINQLVQELGFYRKETP
SPP00000017_1.0.17.genewise -------HNLEMKHLPGADPELVLLSFRYEELERIPLSDMTREEINQLVQELGFYRKETP
SPP00000113_1.0 TEDIQLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQMTRDEINALVQELGFYRKSAP
SPP00000113_1.0.17.exonerate -------HNLEMKHLPGADPELVLLSFRYEELERIPLSDMTREEINQLVQELGFYRKETP
SPP00000113_1.0.17.genewise -------HNLEMKHLPGADPELVLLSFRYEELERIPLSDMTREEINQLVQELGFYRKETP
*** **************. .*:********:***:*** ********** :*
SPP00000017_1.0 DAQVPPEYVWAPAKPPEETSDHADL
SPP00000017_1.0.17.exonerate EAPVPEEFQFAPAKP----------
SPP00000017_1.0.17.genewise EAPVPEEFQFAPAKP----------
SPP00000113_1.0 EAQVPPEYLWAPAKPPEEASEHDDL
SPP00000113_1.0.17.exonerate EAPVPEEFQFAPAKP----------
SPP00000113_1.0.17.genewise EAPVPEEFQFAPAKP----------
:* ** *: :*****
......................................................................................................................................................................................................................................................
BEST PAIRWISE ALIGNMENT
CLUSTAL FORMAT for T-COFFEE Version_7.54, SCORE=100, Nseq=2, Len=145
SPP00000113_1.0 MSILLSPPSLLLLLAALVAPATSTTNYRPDWNRLRGLARGRVETCGGUQLNRLKEVKAFV
SPP00000113_1.0.17.genewise ------------------------------------------------------------
SPP00000113_1.0 TEDIQLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQMTRDEINALVQELGFYRKSAP
SPP00000113_1.0.17.genewise -------HNLEMKHLPGADPELVLLSFRYEELERIPLSDMTREEINQLVQELGFYRKETP
*** *************** .*:********:***:*** **********.:*
SPP00000113_1.0 EAQVPPEYLWAPAKPPEEASEHDDL
SPP00000113_1.0.17.genewise EAPVPEEFQFAPAKP----------
** ** *: :*****
......................................................................................................................................................................................................................................................
RESULTADOS DEL SECISearch
>17:subseq(10556329,10000):[9245,9148] [9148 - 9245] (SECIS on complementary strand) - Free Energy: -34.12 GACAGCAGUAUCCUACCUGCACAGGACAGGAUGAAACUCUCAGCAGAAAGCUCCACAUGCUGAGGGCAGAUGUACUGAGUCCUGGAGGUGGGACAGCU
_[9245,9148].png)
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RESULTADOS DEL Selenoprofiles
Output_id: SelM.2.unaligned
---------- ----------------
-Species Meleagris gallopavo -Taxid 9103
-Target /homes/users/U63748/gallopavo.fa
-Chromosome (-) 17
-Program genewise
-Query name gi|169234774|ref|NP_001108486.1| selenoprotein M precursor [Canis lupus familiaris]
-Query range 65-132 length:142 coverage: 0.48
-Profile range 191-267 length:309 coverage: 0.25 sec_position: [168]
-Average sequence identity with profile: 0.4504 (ignoring gaps: 0.4799)
-State kept
------- alignment -------
Query HNLVMKHLPGADPELVLLGHHYEELE <---Intron---> RIPLSEMTREEINELVQELGFYRKAAPDEAVPPEYLRAPARP
||| |||||||||||||| ||||| < 88bp > |||||/|||||||/|||||||||| |/ || |/ |||/|
Target HNLEMKHLPGADPELVLLSFRYEELE RIPLSDMTREEINQLVQELGFYRKETPEAPVPEEFQFAPAKP
cacgaacccgggcgcgccatatggcg aaccagaacggaaccgcgcgttcagacggcgcggtctgcgac
aatataatcgcacattttgtgaaata gtctgatcgaataattaatgtagaaccacctcaatatcccac
tcggggcgcccctgcggtccatgggg accgccgcgggccgggaggccccggtcactgcggcgtctcga
------- positions -------
Exon 1 10566252 10566329
Exon 2 10566038 10566163
--------- SECIS ---------
>SelM.2.unaligned.esecis:str.1 chromosome:17 strand:- positions:10565476-10565575 species:"Meleagris gallopavo"
target:/homes/users/U63748/gallopavo.fa distance_from_sec_uga:None distance_from_cds:462
GGACAGCAGU AUCCUACC UGCACAGGACAGG AUGAA ACUCUCAGCAG AA AGCUCCAC AUGCUGAGGGC AGAU GUACUGAGUC CUGGAGGU GGGACAGCUG
...((((... .((((((( (...((((((..( .(((( .(((((((((. .. ........ .))))))))). )))) .).....))) ))).)))) ))))..))))
--------- 3' seq --------
Total sequence length available downstream >= 3000
Sequence until first stop codon:
CTGCCCACCCTAATACCCCGCAGAGCTCCTGCAGCTGACAGCAAGACCCTGTCTGAACAGGACAAGAAGGACCGCCCAGACCTGTAA
L P T L I P R R A P A A D S K T L S E Q D K K D R P D L *
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