RetrogeneDB ID: | retro_btau_1792 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:4734784..4735501(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TMEM219 | ||
| Ensembl ID: | ENSBTAG00000021785 | ||
| Aliases: | TMEM219, IGFBP-3R | ||
| Description: | Transmembrane protein 219 [Source:UniProtKB/Swiss-Prot;Acc:Q1JQE1] |
Retrocopy-Parental alignment summary:
>retro_btau_1792
ATGGGCATCTGCCAGGCAGGGCACTACCTGCATCTCTTCCTGGCCCACCACCCACCTCTGGTCTGTGCCACTTTGATCCT
GCTGCTTCTTGGCCTTTCTGGCCTGGGTCTTGGTGGCTTCCTCCTCACCCACAGAACTGACCTGCACAGCCCTGACATCT
CCCAGGACTGGGTCTCCTTCTTGAGATCTTTTGGCCAGCTGGCCCTGTGCCCGGTGAATGGGACAGTCACAAGGAAGGGG
CGTGGGTCTCATGTCGTGGGCTTACTGGCCACCTTGAACTTTGGAGATGGTCCAGACAGGAACAAGACCCAGACATTCCA
AGCCCAGGTCCAGGGTAGCCCGATGGGATTGAAAGGATCTTTTGCAGGAAAGCTGGTGCTCGTTACGGCCAGGGTGACCA
CAGAAAGGACCCCAGGAATCTGCCTGTAGTTTAGTGCTACTCCAGAAATCCTGCCCTCCAGCCAGCCACCGATACCCTGC
TCAGAGGAGGGAGCAAGAAATGCCACCCTGAGCCCTAGAATGGCTGAGGAGTGTGTCAGTGTCTGGAGCCACAAAGGTCT
CGTGCTCATCAAGTTGCTCACCTCGGAGGAGCTGATTCTGTGTGGCTCTCGGCTGCTGGCTTTGGGCTTCTCCCTGATTC
TGTTCTGTGGCCTCTGCTGTCTCACTGCAGCGTGCTTCCATCCGCGCCGGGAGTCCCACTGGTCTAGAACTCAGCTC
ORF - retro_btau_1792 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.96 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGSCQAGHYLHFCLAHHPPLVCATLILLLLGLSGLGLGGFLLTHRTDLRSPDIPQDWVSFLRSFGQLTLC |
| MG.CQAGHYLH..LAHHPPLVCATLILLLLGLSGLGLGGFLLTHRTDL.SPDI.QDWVSFLRSFGQL.LC | |
| Retrocopy | MGICQAGHYLHLFLAHHPPLVCATLILLLLGLSGLGLGGFLLTHRTDLHSPDISQDWVSFLRSFGQLALC |
| Parental | PVNGTVTGKGRGSHIVGLLTTLNFGDGPDRNKTQTFQAQVQGSRMGLKGSFARELVLVTARVTTERTPGT |
| PVNGTVT.KGRGSH.VGLL.TLNFGDGPDRNKTQTFQAQVQGS.MGLKGSFA..LVLVTARVTTERTPG. | |
| Retrocopy | PVNGTVTRKGRGSHVVGLLATLNFGDGPDRNKTQTFQAQVQGSPMGLKGSFAGKLVLVTARVTTERTPGI |
| Parental | CLYFSAIPEILPSSQPPIPCSEEGAGNATLSPRMSEECVGVWSHEGLVLTKLLTSEELTLCGSRLLVLGF |
| CL.FSA.PEILPSSQPPIPCSEEGA.NATLSPRM.EECV.VWSH.GLVL.KLLTSEEL.LCGSRLL.LGF | |
| Retrocopy | CL*FSATPEILPSSQPPIPCSEEGARNATLSPRMAEECVSVWSHKGLVLIKLLTSEELILCGSRLLALGF |
| Parental | FLILFCGLCCLTAACFHPRRESHWSRTRL |
| .LILFCGLCCLTAACFHPRRESHWSRT.L | |
| Retrocopy | SLILFCGLCCLTAACFHPRRESHWSRTQL |
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 .14 RPM | 8 .44 RPM |
| ERP005899_muscle | 0 .00 RPM | 32 .73 RPM |
| SRP017611_brain | 0 .00 RPM | 13 .66 RPM |
| SRP017611_kidney | 0 .00 RPM | 33 .19 RPM |
| SRP017611_liver | 0 .53 RPM | 19 .78 RPM |
| SRP030211_testis | 0 .02 RPM | 27 .88 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1792 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1792 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1792 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000021785 | 1 retrocopy |
retro_btau_1792 ,
|
| Microcebus murinus | ENSMICG00000009088 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000020273 | 1 retrocopy | |
| Oryctolagus cuniculus | ENSOCUG00000006318 | 1 retrocopy |