RetrogeneDB ID: | retro_pabe_2701 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 5:157534228..157535091(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | OBFC1 | ||
| Ensembl ID: | ENSPPYG00000002628 | ||
| Aliases: | None | ||
| Description: | oligonucleotide/oligosaccharide-binding fold containing 1 [Source:HGNC Symbol;Acc:26200] |
Retrocopy-Parental alignment summary:
>retro_pabe_2701
ACTGGAGTTATAAACTGCATCTGCTAGAAAATATTGAGCAATATCAAGTTTTTATCTGCTGCTCCAAATGCAGCAAGAGA
ACTGAGCTTTACCTCAATACTCAAGAAGCTGCAAGACACCATTGAGTAGAGAACAAAAATTGAAACTGGGGACATGTTCT
GAATCAGAGGCTATGTCTACACGTGCAGAGATGAGTGAGAAATTTATGCCACTGCTTATTATAAAGTGGACCATCCAGTG
TGGAACATTCAAATTGCAAGGGTGTTTGGGCTGCCCGTTAATCTACAGGAAAGTTTAGACCAAGCCTTTCCATTGCCCAG
ACTTAGAGAAAGAAGAAGCACTAAGCAATCCAGGTGTCCTGGCCTTCACTAGTCTCATGTGTTTGCTGAGTGAAAAAGCC
GAAGAATTCCCCATGAAGAACAGGGTGCAGACCTTTGACCAGCAGGAGTTGGAAATGGTGGAGCCTTTGCTGTCCCTTGC
TAACCAGCCTGTTACTGACAGCGCCTGCTCGGACCAAGGAAATTTTAAGAAGGATATCACTTTCAAGGCAATTTATAGCA
TATTTTAAAATGCTATGCAACAGCTGCAGGAAAAAGGACTCGTTTTCCAGAAAGATGGTGGTTTTGATAACCTATGCTGT
GTAACCAGAAAAGACAAAGACCTGCATAGGAAAATCCACTGGATAATTCAGGAAGACTGCCAGAAACCAAATCACCTGAA
GAAGGGCTGCCACTTCCTGCACATCTTGGCCTGCACTCACCCTGAGCATCTGCCCAGTTCTAGGTAGGGCTATGTTGCAG
CAAGTTCTGGAGCTCCTGGAGGACCAGAGTGACCTCATCAGCACAATGGAGCACCACTACTCC
ORF - retro_pabe_2701 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.97 % |
| Parental protein coverage: | 77.72 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | TGVINCICWKKL-NTESVSAAPSAARELSLTSQLKKLQETIEQRTKIEIGDTIRVRGSIRTYREEREIHA |
| TGVINCIC.K.L.N....SAAP.AARELS.TS.LKKLQ.TIE.RTKIE.GD....RG...T.R.E.EI.A | |
| Retrocopy | TGVINCIC*KILSNIKFLSAAPNAARELSFTSILKKLQDTIE*RTKIETGDMF*IRGYVYTCRDE*EIYA |
| Parental | AAYYKVDDPVWNIQIARMLELPT-IYRKVYDQPFRSSALEKEEALSNPGALDLPNLTSLLSEKAKEFLME |
| .AYYKVD.PVWNIQIAR...LP..IYRKV...PF....LEKEEALSNPG.L....L..LLSEKA.EF.M. | |
| Retrocopy | TAYYKVDHPVWNIQIARVFGLPV>IYRKV*TKPFHCPDLEKEEALSNPGVLAFTSLMCLLSEKAEEFPMK |
| Parental | NRVQSFYQQELEMVESLLSLANQPVIHSACSDQVNFKKDTTSKAIHSIFKNAIQLLLEKGLVFQKDDGFD |
| NRVQ.F.QQELEMVE.LLSLANQPV..SACSDQ.NFKKD.T.KAI.SIF.NA.Q.L.EKGLVFQKD.GFD | |
| Retrocopy | NRVQTFDQQELEMVEPLLSLANQPVTDSACSDQGNFKKDITFKAIYSIF*NAMQQLQEKGLVFQKDGGFD |
| Parental | NLYYVTREDKDLHRKIHRIIQQDCQKPNHMEKGCHFLHILACAR-LSIRPGLSEAVLQQVLELLEDQSDI |
| NL..VTR.DKDLHRKIH.IIQ.DCQKPNH..KGCHFLHILAC...LSI.P.L..A.LQQVLELLEDQSD. | |
| Retrocopy | NLCCVTRKDKDLHRKIHWIIQEDCQKPNHLKKGCHFLHILACTH>LSICPVLGRAMLQQVLELLEDQSDL |
| Parental | VSTMEHYYT |
| .STMEH.Y. | |
| Retrocopy | ISTMEHHYS |
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 | 3 .37 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .11 RPM |
| SRP007412_heart | 0 .03 RPM | 2 .92 RPM |
| SRP007412_kidney | 0 .00 RPM | 6 .23 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .85 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2701 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2701 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2701 has 5 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3257 |
| Pan troglodytes | retro_ptro_2203 |
| Gorilla gorilla | retro_ggor_2219 |
| Macaca mulatta | retro_mmul_2050 |
| Callithrix jacchus | retro_cjac_1791 |
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018342 | 1 retrocopy | |
| Homo sapiens | ENSG00000107960 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000008979 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000015323 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000015282 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000002628 | 1 retrocopy |
retro_pabe_2701 ,
|
| Pan troglodytes | ENSPTRG00000002919 | 1 retrocopy |