RetrogeneDB ID: | retro_btau_1356 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 4:81908122..81908662(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMA7 | ||
| Ensembl ID: | ENSBTAG00000005127 | ||
| Aliases: | None | ||
| Description: | Proteasome subunit alpha type-7 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBG0] |
Retrocopy-Parental alignment summary:
>retro_btau_1356
ATGAGCTGTAACCGCTCCATCACCGTCTTCTCTCCCAACGGCCACCTCTTCCCAGTGGAGTACTTGCAGGAGGCCATGAA
GAAGGGCTGGACCATGGTCAGTGTTCGAGGAAAAGACATTGTTGTTCTTGGTGTGGAGAAGTCAGTGGCCAAACTGCAGG
ATGAAAGGACAGGGCGGAAGGTCTGTGCTCTGGATGATAATGTCTGCATGGCATTCGCCGACTCACTGCTAACGCAAGGA
TAGTCACCAACAGGGCCCGGGTGGAATGCCAGAGCCACCGGCTGACTGTGGAGGACCTAGTCACCATGGAGTACATCACC
CGTTATATCGCCAGTCTGAAGCAGCGCTACACACAGAGCAAGGAGCGCTGGGGGTTTGGCATCTCTGCCCTCCTTGTGGG
TTTTGACTTTGATGGCACCCCCGACTCTATCAGACTGACCTCCCAGCACATACCATGCCTGGAAAGCCAATGCTGTAGGC
CAGGTTGCCAAGTCAGTGCGTGAATTCCTAGAGAATTATACTGAGGAAGCCATTGAAACC
ORF - retro_btau_1356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.26 % |
| Parental protein coverage: | 73.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MSYDRAITVFSPDGHLFQVEYAQEAVKKGSTAVGVRGKDIVVLGVEKKSVAKLQDERTVRKICALDDNVC |
| MS..R.ITVFSP.GHLF.VEY.QEA.KKG.T.V.VRGKDIVVLGVEK.SVAKLQDERT.RK.CALDDNVC | |
| Retrocopy | MSCNRSITVFSPNGHLFPVEYLQEAMKKGWTMVSVRGKDIVVLGVEK-SVAKLQDERTGRKVCALDDNVC |
| Parental | MAFAG-LTADARIVINRARVECQSHRLTVEDPVTVEYITRYIASLKQRYTQSNGRRPFGISALIVGFDFD |
| MAFA..LTA.ARIV.NRARVECQSHRLTVED.VT.EYITRYIASLKQRYTQS..R..FGISAL.VGFDFD | |
| Retrocopy | MAFAD<LTANARIVTNRARVECQSHRLTVEDLVTMEYITRYIASLKQRYTQSKERWGFGISALLVGFDFD |
| Parental | GT-PRLYQTD-PSGTYHAWKANAIGRGAKSVREFLEKNYTDEAIET |
| GT.PRLYQTD.P..TYHAWKANA.G..AKSVREFLE.NYT.EAIET | |
| Retrocopy | GT<PRLYQTD<PPSTYHAWKANAVGQVAKSVREFLE-NYTEEAIET |
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 | 88 .82 RPM |
| ERP005899_muscle | 0 .00 RPM | 130 .13 RPM |
| SRP017611_brain | 0 .00 RPM | 44 .31 RPM |
| SRP017611_kidney | 0 .00 RPM | 96 .44 RPM |
| SRP017611_liver | 0 .00 RPM | 66 .98 RPM |
| SRP030211_testis | 0 .88 RPM | 21 .49 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1356 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1356 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1356 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000005127 | 1 retrocopy |
retro_btau_1356 ,
|
| Felis catus | ENSFCAG00000003249 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000012281 | 2 retrocopies | |
| Drosophila melanogaster | FBgn0004066 | 1 retrocopy |