RetrogeneDB ID: | retro_sscr_233 | ||
Retrocopy location | Organism: | Pig (Sus scrofa) | |
| Coordinates: | 10:78380586..78381799(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STAU1 | ||
| Ensembl ID: | ENSSSCG00000027444 | ||
| Aliases: | None | ||
| Description: | staufen double-stranded RNA binding protein 1 [Source:HGNC Symbol;Acc:11370] |
Retrocopy-Parental alignment summary:
>retro_sscr_233
GTGAATGGAAGAGAATCAGAAGAAGAAAATCTCAAAAACCTGAAATCATTCAAGTATTTGATATTGCACTTAAATGTAAC
TTGCGAGTGAATTTTTAGGTTTCCCGGGAGAGTGGCCCACCCCACATGAACAGCTTTGTGACCAGGGTGTCAGTTTGGGG
AGTTTATAGTAGAAGGTGAAGGGAAGAGCAAGAATATTCCAAAGGAAAATGCTGGATAGCTGTTCTTGAGGAGCTGAAGA
AGTTACTGTCTCTGCCTATAGTTGAGCAAGTGAAGCCCAGAATCAAAAAGAAAACAGTCAATAATCTGGTTATAGAGCAC
TCAGGAATATGGGCAGGTGATGTATCCCATTAGCAGACTGGCCCAGATCCAGCAGGTGAAAAAGGAGAAGGAGTTATTGT
ACCTTCTTCCCACCAAGTGAGGCCTCCCAAGCTGCAGGGACTTTATGATGCAAGTAAAGGTGGGAAAAAAAACACTGCCA
AAGGATCTGGCACAAAGAAGAACATTACCAAACATAATGCAGCCAAGAGTATGCTGGAGATCCTTAGTTTCAAGGTCCCA
CAGACTCAGCCCACCAAACCAGCCCTCAAATATGAGGAGAGGACACACCAAAAACATCAAGGGATGGAAGAAAAGTAGCC
TTTTTTGAACCTGGTTCTGGGGATGAAAATGGTACTAGCAATTAAGAGGATGAGTCATTATTTTAGCCACATCTTAGTCA
TCAGCACCTGCTTGCTGGAATTCTTCCCAGGGTGCATGAGGTTGCCATGGCCATAGAGGTTATTCAAGGACATCACACCA
AGTATTTCACCAGGATAGCTCCAAAGCCTGCCAAGACCATGGTAACTGCCAAGATAGCCCATGAATTGTGTGGGGACAGC
TTGCCTGCAGCCAAGACCATTTTAAAGAACAACATCTCTTCAGGTCATATTCCCCATGGACTCCTCATGAGACCCTCTTA
GCAGTTGGACTACCTTTCCAGAGTCCAGGGATTCCAGGTTTAATACAAAGACTTCCCCAAAAGCACAAGAATTAATATAT
TATCTCTTATAAATTGTTCCTCTCAGCCACATCTGATCAGCCAGGGTACCAGAAACGATGTGTAGTCCTGCCATGACATG
GCTGCAATAAAAAATTTAAAGTTGCTTCCTGAGTTGGACCAACAAAATACAGAGATGCCAAGAACAGGAAATGGACCAAT
GTCTGTGTATGGG
ORF - retro_sscr_233 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.7 % |
| Parental protein coverage: | 99.51 % |
| Number of stop codons detected: | 8 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | VNGRESEEENLN-KSEISQVFEIALKRNLPVNFEVARESGPPHMKSFVTRVSV-GEFVGEGEGKSKKISK |
| VNGRESEEENL..K.EI.QVF.IALK.NL.VNF.V.RESGPPHM.SFVTRVSV.GEF..EGEGKSK.I.K | |
| Retrocopy | VNGRESEEENLK<KPEIIQVFDIALKCNLRVNF*VSRESGPPHMNSFVTRVSV>GEFIVEGEGKSKNIPK |
| Parental | KNAA-IAVLEELKKLPPLPTVERVK-PRIKKKTKSIVRLQSTQEYGQGMNPISRLAQIQQAKKEKEPEYL |
| .NA..IAVLEELKKL..LP.VE.VK.P..K.K..SI..L.STQEYGQ.M.PISRLAQIQQ.KKEKE..YL | |
| Retrocopy | ENAG<IAVLEELKKLLSLPIVEQVK>PESKRK-QSIIWL*STQEYGQVMYPISRLAQIQQVKKEKELLYL |
| Parental | LLTERGLPRRREFVMQVKV-GNHTAEGSGTNKK-VAKRNAAENMLEILGFKVPQAQPTKPALKSEEKTPI |
| L.T..GLP..R.F.MQVKV.G..........KK...K.NAA..MLEIL.FKVPQ.QPTKPALK.EE.T.. | |
| Retrocopy | LPTK*GLPSCRDFMMQVKV<GXXXTAKGSGTKKNITKHNAAKSMLEILSFKVPQTQPTKPALKYEERTHQ |
| Parental | KKPG-DGRKVTFFEPGSGDENGTSNKEDEFRM-PYLSHQQLPAGILPMVPEVAQAVGVSQGHHTKDFTRV |
| K..G.DGRKV.FFEPGSGDENGTSN.EDE....P.LSHQ.L.AGILP.V.EVA.A..V.QGHHTK.FTR. | |
| Retrocopy | KHQG<DGRKVAFFEPGSGDENGTSN*EDESLF*PHLSHQHLLAGILPRVHEVAMAIEVIQGHHTKYFTRI |
| Parental | APNPAKATVTAMIARELLYGGTSPTAETILKNNISSGHVPHGPLTRPSEQLDYLSRVQGFQVEYKDFPKN |
| AP.PAK..VTA.IA.EL..G...P.A.TILKNNISSGH.PHG.L.RPS.QLDYLSRVQGFQV.YKDFPK. | |
| Retrocopy | APKPAKTMVTAKIAHELC-GDSLPAAKTILKNNISSGHIPHGLLMRPS*QLDYLSRVQGFQV*YKDFPKS |
| Parental | NKNEFVSLINCSSQPPLISHGIGKDVESCHDMAALNILKLLSELDQQNTEMPRTGNGPMSVCG |
| ......SLINCSSQP.LIS.G...DV.SCHDMAA...LKLL.ELDQQNTEMPRTGNGPMSV.G | |
| Retrocopy | TRINILSLINCSSQPHLISQGTRNDV*SCHDMAAIKNLKLLPELDQQNTEMPRTGNGPMSVYG |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP014902_placenta | 0 .00 RPM | 68 .36 RPM |
| SRP014902_testis | 0 .00 RPM | 98 .16 RPM |
| SRP018288_heart | 0 .00 RPM | 55 .66 RPM |
| SRP018288_kidney | 0 .00 RPM | 117 .71 RPM |
| SRP018288_liver | 0 .00 RPM | 87 .31 RPM |
| SRP018288_lung | 0 .00 RPM | 116 .59 RPM |
| SRP018856_adipose | 0 .00 RPM | 118 .34 RPM |
| SRP035408_brain | 0 .00 RPM | 68 .60 RPM |
| SRP035408_liver | 0 .00 RPM | 115 .93 RPM |
Sus scrofa was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_sscr_233 retrocopy.
Sus scrofa was not studied using FANTOM5 data.
retro_sscr_233 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_sscr_233 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000016233 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000016276 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000027444 | 1 retrocopy |
retro_sscr_233 ,
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