RetrogeneDB ID: | retro_pabe_1802 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 20:7794620..7795250(-) | ||
| Located in intron of: | ENSPPYG00000010712 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CCDC84 | ||
| Ensembl ID: | ENSPPYG00000003948 | ||
| Aliases: | None | ||
| Description: | coiled-coil domain containing 84 [Source:HGNC Symbol;Acc:30460] |
Retrocopy-Parental alignment summary:
>retro_pabe_1802
TCTCCCCAGGATTATGCACGATTCAAAAAATCCCTGGTGGAAGACTTGGGTTCCTATGAAGAAAAAGAGGATGAGGTGAC
CAAGGAGATGGCAACTCAGATCCGTGAGGTGGAAGAGAGCTGGCAGGAGGTGGTTCAGTCTGTCTTAGAGGTTGGTTTCC
CTCGGAGGATCCAGACCCCCTTAGCCAGTGCCAGGCACTTTAGTCCCTGGAAGCTGGAAAAGGATGAACAGCCAAGTAGC
TTCCAGCTCACAGCAGCCCTCCAACTCGGACCTGCCACAGCTCCAGAGCTTGACTGGATGGAGACAGGACAATCTCTGAT
ATTCATTGGCCATCAGGATATACCAGGAGCTGGGAACATCCACTCAGGTGCCACACCTCCCTGGATGATCCAAGATAAAG
AATGCATCTCTGGGAACCAACAAACAGGACGGTCCTAAAAATAATTTATTAAAGAAAAGGAAAAAGAGAAGTTGAAGGAA
CTTTCCCCAAACTGAGTTGGGGCCAATTTTGATCACAGCTAAAGGACCAGTGCAGGCTGGCTGCCCTCTTTGGACCGTGT
CTGGAATAATGGATACTGCTGGCAGTTCAGGCATCAGCTCAGAACTGAAGCTGCAGCAATGAACAAGCAG
ORF - retro_pabe_1802 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.67 % |
| Parental protein coverage: | 61.63 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | TPQDYARFKKSMVKGLDSYEEKEDEVIKEMAAQIREVEQSRQEVVRSVLE---PQTVPDPEEGSSAHGSW |
| .PQDYARFKKS.V..L.SYEEKEDEV.KEMA.QIREVE.S.QEVV.SVLE...P.....P.........W | |
| Retrocopy | SPQDYARFKKSLVEDLGSYEEKEDEVTKEMATQIREVEESWQEVVQSVLEVGFPRRIQTPLASARHFSPW |
| Parental | KGINSQVASSSQQPANLDLPP--APELDWMETGPSLTFIGHQDIPGVGNIHSGATPPWMIQD-EYTAGNQ |
| K.......SS.Q..A.L.L.P..APELDWMETG.SL.FIGHQDIPG.GNIHSGATPPWMIQD.E...GNQ | |
| Retrocopy | KLEKDEQPSSFQLTAALQLGPATAPELDWMETGQSLIFIGHQDIPGAGNIHSGATPPWMIQDKECISGNQ |
| Parental | EIGPSYEEFLKEKEKQKLKKLPPDRVGANFDHSSRTSAGWLPSFGRVWNNGRRWQSRHQFKTEAAAMKKQ |
| ..G.S...F.KEKEK.KLK.L.P..VGANFDHS.RTSAGWLPS..RVWNNG..WQ.RHQ..TEAAAM.KQ | |
| Retrocopy | QTGRS*K*FIKEKEKEKLKELSPN*VGANFDHS*RTSAGWLPSLDRVWNNGYCWQFRHQLRTEAAAMNKQ |
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_prefrontal_cortex | 0 .00 RPM | 2 .76 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 4 .86 RPM |
| SRP007412_heart | 0 .03 RPM | 1 .11 RPM |
| SRP007412_kidney | 0 .00 RPM | 3 .78 RPM |
| SRP007412_liver | 0 .00 RPM | 3 .64 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1802 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1802 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_1802 has 3 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_2451 |
| Pan troglodytes | retro_ptro_1416 |
| Gorilla gorilla | retro_ggor_1527 |
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000186166 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000023065 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000007378 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000003948 | 1 retrocopy |
retro_pabe_1802 ,
|
| Pan troglodytes | ENSPTRG00000004360 | 1 retrocopy |