RetrogeneDB ID: | retro_pabe_3656 | ||
Retrocopy location | Organism: | Orangutan (Pongo abelii) | |
| Coordinates: | X:71560962..71562487(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | UHRF2 | ||
| Ensembl ID: | ENSPPYG00000019227 | ||
| Aliases: | None | ||
| Description: | ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:12557] |
Retrocopy-Parental alignment summary:
>retro_pabe_3656
GGGGGTTCTGAAGGGGCATTAAATGAGTGCAAGATAATATCTGTAGATGAAATCTTCAAGACTGAGAAACGTGGAGCCTA
TCCTCTTCCGTTTGCAGATGTAAAGTTTTTAAGGAGAAATAACCCTGAATGTGACCTGTGTGGTGGAGACCCAGATAAGA
AATGCCATTCTTGCTTCTTTCATGTATATGGTGGGAAACATGAACCCAACATGCAGCTTCTATGTGATGAATGTAATGTG
GCTTATCATATTTACTGCTTGAATACACCTTTGGATAAAGTCCCAGAAGAGGAATACTGGTATTGTTCTTCCTGTAAAAC
TGATTCCAGTTAGGTTGTAAAGGCTGGTGAAAGACTCGAGATAAGCGAAAAGAAAGCAAAGATGCCATCCGCTAGTACTG
AAAGCCAGAGAGACTGATGCAGGAGAATGGCTTGTGTTGGTCATATGACAGAATGCACTATTGTCTCTTCTAATCATTAT
GGACCTATTCCTGTTGGATCAACTTGGAGATTTAGAGTTCAGGTGAGTGAAGTATGTGTTCACAGACCTCATGTTGGTGG
ACTTCATGGTCGAAGTAATGATGGAGTTTATTCTCTTGTCTTGGCTGGTGGATTTGTGGATAAAGTTGACCGAGGTGATG
AGTTCTTGTACACTGGAAGTGGCAGTAAAAAGCTTGCTGGTAATAAAAGAATTGGCACACCTTCAGCTGATCAAACATTA
ACAAACACGAACAGGGCATTGGCCCTAAACTGTGATGCTACATTGGGTGATAAAATTGGAGAAGAGTCTCGGAATTGGAG
AGCTGGTAAGCCAGTCAGAGTGATATGCAGTTTTAAAGGGAGGAAGATCAGCAAATATGCTCCTGAAGAAGGCAACAGAT
ATGATGGCATTTATAAGGTAGTGAAATACTGGCCAGAGATTTCATCAAGCCATGGATTCTTGATTTGGCGCTATCTTTTA
AGAAGAGATGATGTTAAACCTGCTCCTTGGACCTCTGAAGGAATAGAATGGTCAAGGAGATTATGTCTACATTTACAGCA
TCCAGCAGGTTACCCTTCAGATAAAGAAAGGAAGAAGACTAAAGGACAGTCAAAGAAGCAGGCCAGTGGAACCACAAAAA
GGCCGATTTCAGATGTCTAAGTGCCTCCAAAGTATACAAAGCATCAGATTCAGCAGGAGCAATTGAGGCTTTTCAACTTA
CTCCTCAACAGCAACATCTCATCAGAGAAGACTGTCAAAATCAGAAGCTGTGGGATGAAGTGCTTGCATATCTTGTGGAA
GGACCAAATTTTCTGAAAAAATTGGAACAATCTTTTATGTGTGTTTGCTGCCAGAAGCTAGTTTACCAGCCTGTGACAAC
TGAGTGCTTCCACAATGTCTGTAAAGATTGCCTACAGTGCTCCTTTAAGGCACAGGTTTTCTCCTGCCCTGCTTGCTGGC
ATGATCTTGGCCAGAATTACATCATAATTCCCCATGAGATTCTGCAGACTCTACTAGACATTTCTTCCCTGGCTACAGCA
AAGGA
ORF - retro_pabe_3656 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.69 % |
| Parental protein coverage: | 64.09 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | GGSEGTLNDCKIISVDEIFKIERPGAHPLSFADGKFLRRNDPECDLCGGDPEKKCHSCSCRVCGGKHEPN |
| GGSEG.LN.CKIISVDEIFK.E..GA.PL.FAD.KFLRRN.PECDLCGGDP.KKCHSC...V.GGKHEPN | |
| Retrocopy | GGSEGALNECKIISVDEIFKTEKRGAYPLPFADVKFLRRNNPECDLCGGDPDKKCHSCFFHVYGGKHEPN |
| Parental | MQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKTDSSEVVKAGERLKMSKKKAKMPSASTESRRDWG |
| MQLLCDECNVAYHIYCLN.PLDKVPEEEYWYC.SCKTDSS.VVKAGERL..S.KKAKMPSASTES.RD.. | |
| Retrocopy | MQLLCDECNVAYHIYCLNTPLDKVPEEEYWYCSSCKTDSS*VVKAGERLEISEKKAKMPSASTESQRD*C |
| Parental | RGMACVGRTRECTIVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFAD |
| R.MACVG...ECTIV.SNHYGP...IPVGSTWRFRVQVSE..VHRPHVGG.HGRSNDG.YSLVLAGGF.D | |
| Retrocopy | RRMACVGHMTECTIVSSNHYGP---IPVGSTWRFRVQVSEVCVHRPHVGGLHGRSNDGVYSLVLAGGFVD |
| Parental | EVDRGDEFTYTGSGGKNLAGNKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRS |
| .VDRGDEF.YTGSG.K.LAGNKRIG.PSADQTLTN.NRALALNCDA.L.DKIG.ESRNWRAGKPVRVI.S | |
| Retrocopy | KVDRGDEFLYTGSGSKKLAGNKRIGTPSADQTLTNTNRALALNCDATLGDKIGEESRNWRAGKPVRVICS |
| Parental | FKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQY |
| FKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFL.WRYLLRRDDV.PAPWTSEGIE.SRRLCL.LQ. | |
| Retrocopy | FKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLIWRYLLRRDDVKPAPWTSEGIEWSRRLCLHLQH |
| Parental | PAGYPSDKEGKKTKGQSKKQPSGTTKRPISDDGCPSASKVYKASDSAEAIEAF-QLTPQQQHLIREDCQN |
| PAGYPSDKE.KKTKGQSKKQ.SGTTKRPISD...P...K..K.....E....F.QLTPQQQHLIREDCQN | |
| Retrocopy | PAGYPSDKERKKTKGQSKKQASGTTKRPISDV*VP--PKYTKHQIQQEQLRLF<QLTPQQQHLIREDCQN |
| Parental | QKLWDEVLAHLVEGPNFLKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG |
| QKLWDEVLA.LVEGPNFLKKLEQSFMCVCCQ.LVYQPVTTECFHNVCKDCLQ.SFKAQVFSCPAC.HDLG | |
| Retrocopy | QKLWDEVLAYLVEGPNFLKKLEQSFMCVCCQKLVYQPVTTECFHNVCKDCLQCSFKAQVFSCPACWHDLG |
| Parental | QNYIMIPNEILQTLLDL-FFPGYSKG |
| QNYI.IP.EILQTLLD..FFPGYSKG | |
| Retrocopy | QNYIIIPHEILQTLLDI<FFPGYSKG |
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 .11 RPM | 20 .51 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 47 .55 RPM |
| SRP007412_heart | 0 .00 RPM | 15 .05 RPM |
| SRP007412_kidney | 0 .03 RPM | 19 .36 RPM |
| SRP007412_liver | 0 .09 RPM | 16 .52 RPM |
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3656 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3656 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_pabe_3656 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Homo sapiens | ENSG00000147854 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000008853 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000009135 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000019227 | 1 retrocopy |
retro_pabe_3656 ,
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