RetrogeneDB ID: | retro_btau_556 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 14:25419913..25420368(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EIF2B1 | ||
| Ensembl ID: | ENSBTAG00000007269 | ||
| Aliases: | None | ||
| Description: | Translation initiation factor eIF-2B subunit alpha [Source:UniProtKB/Swiss-Prot;Acc:Q0IIF2] |
Retrocopy-Parental alignment summary:
>retro_btau_556
GGCATGGACTCTTCAGTGGCCGTGTCGTCGGGCGGTGAGCTCCTGTGCTTCATCAGCCGTACCTCCCTGGAATACTCTGA
TTACTCCAAATGTAGAAAGATCATCATGAGCGGGGAGAGATTTTCCTCAGGAGAATATCACTGTCGAGAAATAAAATTGC
AGATCTATGCCATACTTTGATCAAAGATGGGGCAAGAATATTAATGCACACCTACCCCCAGAGTGGTCCTGAGAGTCTGG
GAAACTGCCCTGGCACCAAGAAGCATTTCAGTGTGTACATTACAGAGTCACAGCCTGACTTATCAGGTAAGATGGCCAAA
GCCCTCTGCCACCTCAGTGTCCCCTTCACTGTGGTCCCTGATGCTGCAGTTGGCTACATCATGGATAACGTGGATCTTGT
CATAGTTGGTGCTGAAGGAGTTGTTGAAAACGGAGGAATCATTAACAAGGTAGGA
ORF - retro_btau_556 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 83.44 % |
| Parental protein coverage: | 50.49 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | GVDSSVAVSSGGELFLRFISLTSLEYSDYSKCKKIMI-ERGEIFLRRISLSRNKIADLCHTFIKDGARIL |
| G.DSSVAVSSGGEL.L.FIS.TSLEYSDYSKC.KI...ERGEIFLRRISLSRNKIADLCHT.IKDGARIL | |
| Retrocopy | GMDSSVAVSSGGEL-LCFISRTSLEYSDYSKCRKIIM<ERGEIFLRRISLSRNKIADLCHTLIKDGARIL |
| Parental | THAY-SRVVLRVLEAAVA-AKKRFSVYITESQPDLSGKKMAKALCHLNVPVTVVLDAAVGYIMEKVDLVI |
| .H.Y..RVVLRV.E.A.A..KK.FSVYITESQPDLSG.KMAKALCHL.VP.TVV.DAAVGYIM..VDLVI | |
| Retrocopy | MHTY>PRVVLRVWETALA<TKKHFSVYITESQPDLSG-KMAKALCHLSVPFTVVPDAAVGYIMDNVDLVI |
| Parental | VGAEGVVENGGIINKIG |
| VGAEGVVENGGIINK.G | |
| Retrocopy | VGAEGVVENGGIINKVG |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 17 .30 RPM |
| ERP005899_muscle | 0 .00 RPM | 14 .73 RPM |
| SRP017611_brain | 0 .00 RPM | 10 .28 RPM |
| SRP017611_kidney | 0 .00 RPM | 15 .65 RPM |
| SRP017611_liver | 0 .00 RPM | 17 .97 RPM |
| SRP030211_testis | 0 .01 RPM | 6 .09 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_556 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_556 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_556 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000007269 | 1 retrocopy |
retro_btau_556 ,
|
| Sus scrofa | ENSSSCG00000009770 | 1 retrocopy |