RetrogeneDB ID: | retro_mmul_615 | ||
Retrocopy location | Organism: | Rhesus macaque (Macaca mulatta) | |
| Coordinates: | 10:67413627..67414413(+) | ||
| Located in intron of: | ENSMMUG00000023622 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | FBXW4 | ||
| Ensembl ID: | ENSMMUG00000006753 | ||
| Aliases: | None | ||
| Description: | F-box/WD repeat-containing protein 4 [Source:RefSeq peptide;Acc:NP_001244875] |
Retrocopy-Parental alignment summary:
>retro_mmul_615
CGACCTGCTCTGGGAGTCTTTGCTGGGCATGATGAGGACATTTGCCACTTTGTGCTGGCCAGCTTGCATATTGTCAGTGC
AGGAGGAGATGGGAAGATTGGCGTTGGTAAGATTCACAGCACCTTCACTGTCAAGTACTCGGCTCATGGACAGGAGGTGA
ACTATGTGGATTGCAAAGGGGGCATCACTGTGAGTGGCTCCAGGGACGGGATGGCCAAGGTGTGGCCTTTGGCCTCAGGC
CGGCTGGAGCAGTGTTTACACACCATCCAGATTGAAGACTGAGTCTGGTCCATTGCTATCAGCCCATTACTCAGCTCTTT
TGTGACAGGGACGGCTTGTTGCGGGCACTTCTCACCCCTGAGAGTCTGGGACCTCAACAGTGGGCAGCTGATGACATACT
TGGGCAGTGACTTTCTCCCAGGGGCTGGGGTGCTGGATGTCATGTATGAGTCCCCTTTCACACTGCTGTCCTGTGGCTAT
GACACCTACGTTCGCTACTGGGACCTCTGCACCAGTGTCCGGAAAGGTGTCATGGAGTGGGAGGAGCCCCACAGCAGCAC
CCTGTACTGTCTGCAGACAGATGGCAACCACTTGCTGGCCACAGGTTCCTCCTACTACAGTGTTGTACGGCTGTGAGACC
GGTGTCAAAGGGCCTGCGGCTGCCTGCACACCTTCCCGCTGACATCAACCCCCTCCAGCAGCCCTGTGTACTGCCTGCGT
CTCACCACCAAGCATCTCTATGCTGCACTGTCTTATGACCTCCACGTCCTGGATTTTCAAAACCCA
ORF - retro_mmul_615 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.93 % |
| Parental protein coverage: | 63.41 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | RRPLGVFAGHDEDVCHFVLANSHIISAGGDGKIGVHKIHSTFTVKYSAHEQEVNCVDCKGGIIVSGSRDR |
| R..LGVFAGHDED.CHFVLA..HI.SAGGDGKIGV.KIHSTFTVKYSAH.QEVN.VDCKGGI.VSGSRD. | |
| Retrocopy | RPALGVFAGHDEDICHFVLASLHIVSAGGDGKIGVGKIHSTFTVKYSAHGQEVNYVDCKGGITVSGSRDG |
| Parental | TAKVWPLASGRLGQCLHTIQTEDRVWSIAISPLLSSFVTGTACCGHFSPLRIWDLNSGQLMTHLGSDFPP |
| .AKVWPLASGRL.QCLHTIQ.ED.VWSIAISPLLSSFVTGTACCGHFSPLR.WDLNSGQLMT.LGSDF.P | |
| Retrocopy | MAKVWPLASGRLEQCLHTIQIED*VWSIAISPLLSSFVTGTACCGHFSPLRVWDLNSGQLMTYLGSDFLP |
| Parental | GAGVLDVMYESPFTLLSCGYDTYVRYWDLRTSVRKCVMEWEEPHDSTLYCLQTDGNHLLATGSSYYGVVR |
| GAGVLDVMYESPFTLLSCGYDTYVRYWDL.TSVRK.VMEWEEPH.STLYCLQTDGNHLLATGSSYY.VVR | |
| Retrocopy | GAGVLDVMYESPFTLLSCGYDTYVRYWDLCTSVRKGVMEWEEPHSSTLYCLQTDGNHLLATGSSYYSVVR |
| Parental | LWDRRQRA--CLHAFPLTSTPLSSPVYCLRLTTKHLYAALSYNLHVLDFQNP |
| L.DR.QRA..CLH.FPLTSTP.SSPVYCLRLTTKHLYAALSY.LHVLDFQNP | |
| Retrocopy | L*DRCQRACGCLHTFPLTSTPSSSPVYCLRLTTKHLYAALSYDLHVLDFQNP |
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 |
|---|---|---|
| SRP007412_brain | 0 .22 RPM | 16 .81 RPM |
| SRP007412_brain_prefrontal_cortex | 0 .87 RPM | 38 .55 RPM |
| SRP007412_cerebellum | 0 .52 RPM | 19 .63 RPM |
| SRP007412_heart | 0 .00 RPM | 33 .45 RPM |
| SRP007412_kidney | 1 .06 RPM | 23 .36 RPM |
| SRP007412_liver | 0 .04 RPM | 28 .06 RPM |
| SRP007412_testis | 0 .08 RPM | 13 .38 RPM |
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_615 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_615 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmul_615 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macaca mulatta | ENSMMUG00000006753 | 1 retrocopy |
retro_mmul_615 ,
|
| Pongo abelii | ENSPPYG00000002586 | 1 retrocopy |