RetrogeneDB ID: retro_ptro_1468

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:17163696..17165134(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: UBE3A
• Ensembl ID: ENSPTRG00000006829
• Aliases: None
• Description: None

Sequence

>retro_ptro_1468
GATTTTAAAGGTGTGACTTACTTAACAGAAGAGAAGGTATATGAAATTACTGAATTATGTAGAGAAAGAGAGGATTATTC
CCCCTTAACTGTGTTATTGGAAGAGTTTTTTCTAGTGCTGAGGCATTGGTAGAGAGCTTCCGGAAAGCTAAACAACACAC
CAAGGAAGAACTGAAGTCTCTTCAAGCAAAGGATGAAGAGAAGAATGAAAATGAAAAGGGAAAAGCTGCATGTTCTGCTG
CTGCTATGGAAGAAGACTCAGAAGCATCTTCCTCAAGCACAGGTGATAGCTCACAGGGAGAAAACAATTTGCAAAAATTA
GGCCCTGATGATGTGTCTGTGGATACTGATGCCATTAGAAGGGTCTACACCAGATTGCTCTCTAATAAAAAAATTGAAAT
TGCCTCTCTCAATGCACTTGTATATTTGTCACCTAACGTGGAATGTGACTTGATGTATCACAAGGTATACTCTCAAGATC
CTAATTATCTGAATTTGTTCATTATAGTAATGGAGAACAGAAATCTCCACAGTCCTGAATATCTGGAAATGGCTTTGCCA
TTATTTTGCAAAGCAGTGAGCAAGCTACCCCTTGCAGCCCAAGGAAAACTGATCAGACTGTGGTCTAAATACAGTGCAGA
CCAGATTCAGAGAATGATGGAGACATTTCAGCAACTTACTACTTACAAAGTCATAAGCAATGAATTTAATAGTCAAAATC
TAGTGAATGATGATGATGCCATTGTTGCTGCTTCGAAGTGCTTGAAAGTGATTTACTATGCAAATGGTAGTGGGAGGGGA
AGTGGACACAAATCACAATGAGGAAGATGATGAAGAGCCCATCCCTGAGTCCAGTGAGCTGACACTTCAGGAGCTTTTGG
AAGAAGAGAGAAGAAACAAGAAAGGTCCTTGAGTGGACCCCCTGGAAAATGAACTTGGTGTTAAAACCCTGGATTGTCAA
AAATCCCTTATCCCTTTTGAAGAGTTTATTAATGAACCACTGAAAGAGGTTCTAGAAATGCATAAAAATTATACTGTTTT
CAAAGTAGAAACAGAACAAATTCTCTTTTATGACATACCCCTTTTTAGTGTATGCTGTCACAAAGAATTTGGGATAATAT
TATGACAATAGGATTCCCATGTACAGTGAACGAAGAATCACTGTTCTCTACAGCTTAGTTCAAGGACAGCAGTTGAATCC
ATATATGAGACTCATTGTTAGATGTGACCATATCATAGATGATGCACTTGTCCGGCTAGAGATGATCACTAAGGAAAATC
CTGCAGACTTGAAGCAGTTCTATGTGGAATTTGAAGGAGAACAAGGTGAGGGAGGTGTTTCCAAATAATTTTTTCAGCTG
GTTGTGGAGGAAATCTTCAATCCAGATATTGGTATGTTCACGTACGATGAACTTACAAATTTGTTTTGATTTGATCCA

Alignment

ORF - retro_ptro_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.63 %
• Parental protein coverage: 55.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DFKDVTYLTEEKVYEILELCREREDYSPLIR-VIGRVFSSAEALVQSFRKVKQHTKEELKSLQAKDEDKD
          DFK.VTYLTEEKVYEI.ELCREREDYSPL...VIGRVFSSAEALV.SFRK.KQHTKEELKSLQAKDE.K.
Retrocopy DFKGVTYLTEEKVYEITELCREREDYSPLTV<VIGRVFSSAEALVESFRKAKQHTKEELKSLQAKDEEKN

Parental  EDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNA
          E.EK.KAACSAAAMEEDSEASSS..GDSSQG.NNLQKLGPDDVSVD.DAIRRVYTRLLSN.KIE.A.LNA
Retrocopy ENEKGKAACSAAAMEEDSEASSSSTGDSSQGENNLQKLGPDDVSVDTDAIRRVYTRLLSNKKIEIASLNA

Parental  LVYLSPNVECDLTYHNVYSRDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWS
          LVYLSPNVECDL.YH.VYS.DPNYLNLFIIVMENRNLHSPEYLEMALPLFCKA.SKLPLAAQGKLIRLWS
Retrocopy LVYLSPNVECDLMYHKVYSQDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAVSKLPLAAQGKLIRLWS

Parental  KYNADQIRRMMETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMVYYAN-VVGGEVDTNHNEEDDE
          KY.ADQI.RMMETFQQL.TYKVISNEFNS.NLVNDDDAIVAASKCLK..YYAN.VVGGEVDTNHNEEDDE
Retrocopy KYSADQIQRMMETFQQLTTYKVISNEFNSQNLVNDDDAIVAASKCLKVIYYAN>VVGGEVDTNHNEEDDE

Parental  EPIPESSELTLQELLGEERRNKKGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFK
          EPIPESSELTLQELL.EERRNKKGP.VDPLE.ELGVKTLDC.K.LIPFEEFINEPL.EVLEM.K.YT.FK
Retrocopy EPIPESSELTLQELLEEERRNKKGP*VDPLENELGVKTLDCQKSLIPFEEFINEPLKEVLEMHKNYTVFK

Parental  VETENKFSFMTCP-FILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDAL
          VETE....F...P.F...AVTKNLG.YYDNRI.MYSERRITVLYSLVQGQQLNPY.RL.VR.DHIIDDAL
Retrocopy VETE-QILFYDIP>FLVYAVTKNLG*YYDNRIPMYSERRITVLYSLVQGQQLNPYMRLIVRCDHIIDDAL

Parental  VRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFWFNP
          VRLEMI..ENPADL.KQ.YVEFEGEQG..EGGVSK.FFQLVVEEIFNPDIGMFTYDE.T.LF.F.P
Retrocopy VRLEMITKENPADL-KQFYVEFEGEQG--EGGVSK*FFQLVVEEIFNPDIGMFTYDELTNLF*FDP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.70 RPM
SRP007412_cerebellum	0.04 RPM	41.12 RPM
SRP007412_heart	0.00 RPM	44.27 RPM
SRP007412_kidney	0.00 RPM	31.91 RPM
SRP007412_liver	0.00 RPM	15.55 RPM
SRP007412_testis	0.00 RPM	85.99 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1468 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1468 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2523
Gorilla gorilla	retro_ggor_1575
Pongo abelii	retro_pabe_1855

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003764	1 retrocopy	retro_cjac_2048,
Homo sapiens	ENSG00000114062	1 retrocopy	retro_hsap_2523,
Gorilla gorilla	ENSGGOG00000003955	1 retrocopy	retro_ggor_1575,
Pongo abelii	ENSPPYG00000006272	1 retrocopy	retro_pabe_1855,
Pan troglodytes	ENSPTRG00000006829	1 retrocopy	retro_ptro_1468 ,