RetrogeneDB ID: | retro_btau_1423 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 5:50710795..50711143(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | APH1B | ||
| Ensembl ID: | ENSBTAG00000010641 | ||
| Aliases: | None | ||
| Description: | gamma-secretase subunit APH-1B [Source:RefSeq peptide;Acc:NP_001178332] |
Retrocopy-Parental alignment summary:
>retro_btau_1423
TTGAGGGTGTCCGTCCTTTTTGACTGCACTTTCATTGCCATTGGTCCTGGGCTTGCCCTCTGCATTGCACCATCGTCACT
GAGTCTTTGAGCATCATCTTCCTCACCATCAGAGCTTTCTTCTGCTTATGTCTCTGTGGCTTTCCTCCCTTGTTTGGTTC
AAGGCAGCAACCATTACTGACAACTAAGATGGACCAATACAGAAATATCTGCTGATCTTAGGAGTGTTAGTCTCAGTCCT
CATCCAAGAAATGTTCTGGTTTGCATATTATGAACTTAAAAGAGCCGGTGAAGGTTTGAAGAGTATAAACCCAGATGAAA
CAGCACCCTCGGTGGATTGCTGGCTTAT
ORF - retro_btau_1423 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.64 % |
| Parental protein coverage: | 54.63 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MTAAVFFGCAFIAFGPALALYIF-TIVTEPLRIIFLIIGAFFWL-VSLLFSSLIWFTTATLIGNKDEPRE |
| ....V.F.C.FIA.GP.LAL.I..TIVTE.L.IIFL.I.AFF.L..SL..SSL.WF..AT...N.D.P.. | |
| Retrocopy | LRVSVLFDCTFIAIGPGLALCIA<TIVTESLSIIFLTIRAFFCL<MSLWLSSLVWFKAATITDN*DGPIQ |
| Parental | KYLLIFGVLISVLIQEMFRFAYYKLLKKASEGLKTINPYEKAPSM-RLLAY |
| KYLLI.GVL.SVLIQEMF.FAYY..LK.A.EGLK.INP.E.APS...LLAY | |
| Retrocopy | KYLLILGVLVSVLIQEMFWFAYYE-LKRAGEGLKSINPDETAPSV<GLLAY |
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 | 0 .00 RPM |
| ERP005899_muscle | 0 .00 RPM | 0 .42 RPM |
| SRP017611_brain | 0 .00 RPM | 3 .97 RPM |
| SRP017611_kidney | 0 .00 RPM | 3 .38 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .53 RPM |
| SRP030211_testis | 0 .09 RPM | 19 .52 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1423 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1423 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1423 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000010641 | 1 retrocopy |
retro_btau_1423 ,
|
| Sus scrofa | ENSSSCG00000004567 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000006865 | 2 retrocopies |