RetrogeneDB ID: | retro_btau_477 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 12:71240811..71241171(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CD164 | ||
| Ensembl ID: | ENSBTAG00000017992 | ||
| Aliases: | None | ||
| Description: | Sialomucin core protein 24 [Source:UniProtKB/Swiss-Prot;Acc:Q2YDH0] |
Retrocopy-Parental alignment summary:
>retro_btau_477
ACCTCCCCGGTTCCTGATGTGACTACAGTCCAGTTTTACTAAGCACCACGATAGCCCCAGTACCGCCACTCCTCAGGGAC
ACTTCTCCAGCACCAGAAATCCGGGAAACCATAACAGCTGTGTTTCCTGTTTTGATGCTAAGGCTATTAATACTACCTGC
TTTTGGACTGAATGAAAGGTAAATGCTACTGTTTACATAATTCAGAGTTAGTCACTGCCAGTTGGTAAACACAGAATTCT
TTCTGTGCCCGCTGTCACACCATTGCCAACCAATTCGAGAGCTAACACCACAACTCTGCCTTCCCCTCCACAGCTCCCAC
CGCAGCTGCCACATCAGGTGTAACTAAAACCACTAACTCT
ORF - retro_btau_477 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.49 % |
| Parental protein coverage: | 58.08 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | SSPPPTTTTV-PVS-PTTLSP----LPVTTPAPDIC-GSRNSCVSCVDG---NATCFWIE-CKGKSYCSD |
| .SP.P..TTV.PV...TT..P....L..T.PAP.I..G..NSCVSC.D....N.TCFW.E..KGK.YC.. | |
| Retrocopy | TSPVPDVTTV<PVLLSTTIAPVPPLLRDTSPAPEIR<GNHNSCVSCFDAKAINTTCFWTE<MKGKCYCLH |
| Parental | NST-AGDCKVVNTTGF-CSVPTTTPTPTNSTAKTTTLPS-TTTTSTTATTSGTTNTTLS |
| NS.....C..VN.T.F..SVP..TP.PTNS.A.TTTLPS...T..T.A.TSG.T.TT.S | |
| Retrocopy | NSE<VSHCQLVN-TEF<LSVPAVTPLPTNSRANTTTLPS<PSTAPTAAATSGVTKTTNS |
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 | 67 .55 RPM |
| ERP005899_muscle | 0 .00 RPM | 132 .87 RPM |
| SRP017611_brain | 0 .00 RPM | 24 .99 RPM |
| SRP017611_kidney | 0 .00 RPM | 347 .87 RPM |
| SRP017611_liver | 0 .00 RPM | 143 .16 RPM |
| SRP030211_testis | 0 .06 RPM | 75 .40 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_477 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_477 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_477 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000017992 | 3 retrocopies |
retro_btau_477 , retro_btau_479, retro_btau_503,
|
| Macaca mulatta | ENSMMUG00000007011 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000015500 | 2 retrocopies | |
| Tursiops truncatus | ENSTTRG00000004181 | 2 retrocopies |