RetrogeneDB ID: | retro_pabe_2715 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | 5:5440477..5441183(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ppy-mir-1224 | ||
| Ensembl ID: | ENSPPYG00000014350 | ||
| Aliases: | None | ||
| Description: | ppy-mir-1224 [Source:miRBase;Acc:MI0015193] |
Retrocopy-Parental alignment summary:
>retro_pabe_2715
AGCCTGACAGCCTCTGTGAAGATGAATGTGCTGCTCTTCGCCCCTGGGTTACTGTTTCTTCTTCTCACACAGTTTGGCTG
CCATGGGGCCTTCCGCAAGCTGGGCATTTGTGTTGGCCTTCAGGTGGTGCTGGGGCTGCCCTTCCTGCTGGAGAAGCCCA
CTGGCTACCTGTCTCGCTCCTTTGACCTTGGCCGCCAGTTTCTGTTCTGCTGGACAGTGAACCGGCGCTTCCTCCCAGGG
GCTCTCTGCCTGCACCATGCCTTCCATCTGGCCCTGCTGGCCACCCACCTCACCTTGCTCTTGCTGTTTACCCTCTACGG
GTGGCACAGGATGGGGGAATGTATCTTGTCACTGAGGAAGGATCCCTCCAAAAGGAAGGTTCCACCCCACCCCTTCATAC
CCAACCAGATCGTTTCTACCCTCTTCACCTCTAACTTCATTGGCATCTGCTTCAGCCACCCCCCTCCACTACCAGTTCTA
TGTCTGGTATTTCCACACACTGCCCTACCTCCTGTGGGCCAGGACTGCACACTGGCTCACACACCTGCTCAGGTTGCTGG
TGCTGGGGCTCATGGAGCTCTCCTGGAACACATACCCCTCCACATCCTGCAACTCTGCTGCCCAGCATGTGTGCCATGCT
ATCCTCTTACTGCAGCTCTGGCTGGGCCTGCAGCCATTCCCCAAGAGCATCCAATGCATCAAGAAA
ORF - retro_pabe_2715 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.63 % |
| Parental protein coverage: | 53.65 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SLAVSVKMNVLLFAPGLLFLLLTQFGFRGALPKLGICAGLQVVLGLPFLLENPIGYLSRSFDLGRQFLFR |
| SL..SVKMNVLLFAPGLLFLLLTQFG..GA..KLGIC.GLQVVLGLPFLLE.P.GYLSRSFDLGRQFLF. | |
| Retrocopy | SLTASVKMNVLLFAPGLLFLLLTQFGCHGAFRKLGICVGLQVVLGLPFLLEKPTGYLSRSFDLGRQFLFC |
| Parental | WTVNWRFLPEALFLHRAFHLALLTAHLTLLLLFALCRWHRTGESILSLLRDPSKRKVPPQPLTPNQIVST |
| WTVN.RFLP.AL.LH.AFHLALL..HLTLLLLF.L..WHR.GE.ILSL..DPSKRKVPP.P..PNQIVST | |
| Retrocopy | WTVNRRFLPGALCLHHAFHLALLATHLTLLLLFTLYGWHRMGECILSLRKDPSKRKVPPHPFIPNQIVST |
| Parental | LFTSNFIGICFSR-SLHYQFYVWYFHTLPYLLWATPARWLTHLLRLLVLGLIELSWNTYPSTSCSSAALH |
| LFTSNFIGICFS...LHYQFYVWYFHTLPYLLWA..A.WLTHLLRLLVLGL.ELSWNTYPSTSC.SAA.H | |
| Retrocopy | LFTSNFIGICFSH>PLHYQFYVWYFHTLPYLLWARTAHWLTHLLRLLVLGLMELSWNTYPSTSCNSAAQH |
| Parental | VCHAVILLQLWLGPQPFPKSTQHSKK |
| VCHA..LLQLWLG.QPFPKS.Q..KK | |
| Retrocopy | VCHAILLLQLWLGLQPFPKSIQCIKK |
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 | 16 .53 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 11 .31 RPM |
| SRP007412_heart | 0 .00 RPM | 5 .06 RPM |
| SRP007412_kidney | 0 .00 RPM | 17 .97 RPM |
| SRP007412_liver | 0 .00 RPM | 20 .41 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2715 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2715 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_2715 has 2 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_3286 |
| Macaca mulatta | retro_mmul_2063 |
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000214160 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000018951 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000006230 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000014350 | 1 retrocopy |
retro_pabe_2715 ,
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