RetrogeneDB ID: | retro_btau_853 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 2:6835863..6836214(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AKIRIN1 | ||
| Ensembl ID: | ENSBTAG00000004715 | ||
| Aliases: | None | ||
| Description: | akirin-1 [Source:RefSeq peptide;Acc:NP_001094706] |
Retrocopy-Parental alignment summary:
>retro_btau_853
CCGGAGCAAATTTTTCAGAGCATCAAGCAAGACTACAGTCACTATCAGAAGTGGAGTCATTCAGAAGTTGTTCTTAAAGC
TTGTATTTTGGGAATTCATCTCCCTCCTCGGCATGCCCAGCATCTAGGTTCTCCAGGTTCCTCCTGTATGAACACCAATC
AGTCCTCCTCCATCGTCCAACAAGTTGCAATTATGTGTAAGCATCTCTTACAAGACTAAAAAGATCATATTTGGGAAGGG
TATGAGCAAATCCTCTACAGCTAATTAGCAGAATGGTATGAATCTTTTGTGAAATTCACACATCGTGAGATTAGGCCACG
AGATGGGAGGAGGCCAACAAATTAAGTGTCC
ORF - retro_btau_853 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.67 % |
| Parental protein coverage: | 62.5 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PEQIFQNIKQEYSRYQRWRHLEVVLNQSEACTSESQPHSSTLTAPSSPGSSWMKKDQPTFTLRQVGIICE |
| PEQIFQ.IKQ.YS.YQ.W.H.EVVL............H...L..P...GSS.M...Q......QV.I.C. | |
| Retrocopy | PEQIFQSIKQDYSHYQKWSHSEVVLKACILGIHLPPRHAQHLGSP---GSSCMNTNQSSSIVQQVAIMCK |
| Parental | RLLKDYEDKIREEYEQILNTKLAEQYESFVKFTHDQIMRRYGTRPTSYVS |
| .LL.D..D.I.E.YEQIL...LAE.YESFVKFTH..I..R.G.RPT..VS | |
| Retrocopy | HLLQD*KDHIWEGYEQILYS*LAEWYESFVKFTHREIRPRDGRRPTN*VS |
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 | 43 .19 RPM |
| ERP005899_muscle | 0 .00 RPM | 51 .52 RPM |
| SRP017611_brain | 0 .00 RPM | 86 .79 RPM |
| SRP017611_kidney | 0 .00 RPM | 75 .04 RPM |
| SRP017611_liver | 0 .00 RPM | 23 .94 RPM |
| SRP030211_testis | 0 .03 RPM | 164 .80 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_853 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_853 was not experimentally validated.