RetrogeneDB ID: | retro_btau_479 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 12:75375212..75375636(+) | ||
| 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_479
ACCTCTCCAGCCCCAGAAATCTGGGAAACCACAACAGCTGTGTTTCCTGTTTTGATGCTAAGACTGCTAATACTACCTGC
TTTTGGACTGAATGAAAGGTAAGACCTACTGTTTACATAATTCAAAGTTAGTGACTGCCAGGTGGTGAACACAGAATTCT
TTCTGTATCTGTGCCTGCTGTCACACCATTGCCAACCAATTTGAGAGCTAACACCACAACTCTGCCTTTCCCTCCACAGC
TCCCACCGCAGCTGCCACATCAGGTGTAACTAAAACCACTAACTCTGAGCTCACAACCCATGCCAAAGTCTGCCTCTGAT
GCAGCCAGGTTCTTTGGAGGAGCTGTCCTTTCTTGGGTGTGTAGGCTGTAATTTTCTTTCTCTATAGATTTGCAAATCTA
AAAACACAAAATTACCACACCCTA
ORF - retro_btau_479 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.94 % |
| Parental protein coverage: | 70.71 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 8 |
Retrocopy - Parental Gene Alignment:
| Parental | TTPAPDI-CGSRNSCVSCVDG---NATCFWIE-CKGKSYCSDNST-AGDCKVVNT-TGFC-SVPTTT--P |
| T.PAP.I..G..NSCVSC.D....N.TCFW.E..KGK.YC..NS....DC.VVNT...FC.SVP..T..P | |
| Retrocopy | TSPAPEI<LGNHNSCVSCFDAKTANTTCFWTE<MKGKTYCLHNSK<VSDCQVVNT>NSFC>SVPAVTPLP |
| Parental | TPTNSTAKT-TTLPSTTTTSTTATTSGTTNT-TLSPTIQPTRKSTFDAASFIGGIVL-VLGVQAVIFFLY |
| T.......T....PST..T...AT...T..T.TLS...QP..KS..DAA.F.GG.VL..LGV.AVIFFLY | |
| Retrocopy | TNLRANTTT<SAFPSTAPTAA-ATSGVTKTT>TLSS--QPMPKSASDAARFFGGAVL<FLGV*AVIFFLY |
| Parental | KFCKSKERNYHTL |
| .F...K..NYHTL | |
| Retrocopy | RFANLKTQNYHTL |
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 .00 RPM | 75 .40 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_479 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_479 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_479 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 |