RetrogeneDB ID: | retro_btau_1350 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 4:59919916..59920467(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AIP | ||
| Ensembl ID: | ENSBTAG00000010478 | ||
| Aliases: | None | ||
| Description: | AH receptor-interacting protein [Source:RefSeq peptide;Acc:NP_898905] |
Retrocopy-Parental alignment summary:
>retro_btau_1350
GGCATCACCTAGATGCAGGAGCACAATTCCCTGGGCCATGCTGATCTGGATACCCTGCAGCAGAAGGCCTAGCCTCTCAT
CTTTGACATTGAGATGCTTAAGATGGAGAATCCTGGCACATATCAGCAGGACCCATGGGCAATGACAGTTGAGGAGAAGG
CAAAGGCAATGCCAGTCATCCACCAGGAGGGCAACTGGTTGTACCTCGAAGGCCATGTGAAGGAGGCTGCTGCCAAATGG
TATGAGGCCATCGCCTGTGTCAAGAACCTTCAGATAAAAGAACAGTCTGAGTCCCCTGACAGAATCCAATTGGATCAGCA
GATCCCACTGCTGTTGCTCAACTACTGTTAGTGCAAGCTGATGGTGGAAGAGTATCAGAAGTGCTGGGCCAGTGCTCCTC
CATCCTCAGTAAGTATGATGACAATGTCAAGGCCTACTTCAAGTACATCAAGGCACATGCATCAATGTGGAACACTCAAG
AGGCCCAGGCTGACTTTGCCAAGGTGCTGGAGCTGGGACCCACCCTGGCGACTATGGTGAGCCCTGAGCTG
ORF - retro_btau_1350 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 78.38 % |
| Parental protein coverage: | 55.76 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GIAQMHEHNSLGHADLDALQQNPQPLIFDIEMLKVENPGTYQQDPWAMTDEEKAKAVPVIHQEGNRLYRE |
| GI..M.EHNSLGHADLD.LQQ...PLIFDIEMLK.ENPGTYQQDPWAMT.EEKAKA.PVIHQEGN.LY.E | |
| Retrocopy | GIT*MQEHNSLGHADLDTLQQKA*PLIFDIEMLKMENPGTYQQDPWAMTVEEKAKAMPVIHQEGNWLYLE |
| Parental | GHVKEAAAKYYDAIACLKNLQMKEQPGSPDWIQLDQQITPLLLNYCQCKLVAEEYY-EVLDHCSSILNKY |
| GHVKEAAAK.Y.AIAC.KNLQ.KEQ..SPD.IQLDQQI..LLLNYC.CKL..EEY..EVL..CSSIL.KY | |
| Retrocopy | GHVKEAAAKWYEAIACVKNLQIKEQSESPDRIQLDQQIPLLLLNYC*CKLMVEEYQ<EVLGQCSSILSKY |
| Parental | DDNVKAYFKRGKAHAAVWNAQEAQADFAKVLQLDPALAPVVSREL |
| DDNVKAYFK..KAHA..WN.QEAQADFAKVL.L.P.LA..VS.EL | |
| Retrocopy | DDNVKAYFKYIKAHASMWNTQEAQADFAKVLELGPTLATMVSPEL |
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 | 3 .39 RPM |
| ERP005899_muscle | 0 .00 RPM | 14 .78 RPM |
| SRP017611_brain | 0 .00 RPM | 20 .56 RPM |
| SRP017611_kidney | 0 .00 RPM | 32 .07 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .53 RPM |
| SRP030211_testis | 0 .00 RPM | 9 .68 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1350 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1350 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1350 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000010478 | 1 retrocopy |
retro_btau_1350 ,
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