RetrogeneDB ID: retro_ggor_1575

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 21:19364747..19366185(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE3A
• Ensembl ID: ENSGGOG00000003955
• Aliases: None
• Description: None

Sequence

>retro_ggor_1575
GATTTTAAAGATGTGACTTACTTAACAGAAGAGAAGGTATATGAAATTACTGAATTATGTAGAGAAAGAGAGGATTATTC
CCCCTTAACTGTGTTATTGGAAGAGTTTTTTCTAGTGCTGAGGCATTGGTAGAGAGCTTCCGGAAAGCTAAACAACACAC
CAAGGAAGAACTGAAGTCTCTTCAAGCAAAGGATGAAGAGAAGAATGAAAATGAAAAGGCAAAAGCTGCATGTTCTGCTG
CTGCTATGGAAGAAGACTCAGAAGCATCTTCCTCAAGCACAGGTGATAGCTCACAGGGAGACAACAGTTTGCAAAAATTA
GGCCCTGATGATGTGTCTGTGGATACTGATGCCATTAGAAGGGTCTACACCAGATTGCTCTCTAATGAAAAAACTGAAAT
TGCCTTTCTCAATGCACTTGTATATTTGTCACCTAACGTGGAATGTGACTTGATGTATCACAAGGTATACTCTCAAGATC
CTAATTATCTGAATTTGTTCATTATAGTAATGGAGAACAGAAATCTCCACAGTCCTGAATATCTGGAAATGGCTTTGCCA
TTATTTTGCAAAGCAGTGAGCAAGCTACCCCTTGCAGCCCAAGGAAAACTGATCAGACTGTGGTCTAAATACAATGCAGA
CCAGATTCGGAGAATGGTGGAGACATTTCAGCAACTTACTACTTACAAAGTCATAAGCAACGAATTTAACAGTCAAAATC
TAGTGAATGATGATGATGCCATTGTTGCTGCTTCGAAGTGCTTGAAAGTGATTTACTATGCAAATGGTAGTGGGAGGGGA
AGTGGACACAAATCACAATGAGGAAGATGATGAAGAGCCCATCCCTGAGTCCAGTGAGCTGACACTTCAGGAGCTTTTGG
AAGAAGAGAGAAGAAACAAGAAAGGTCCTTGAGTGGACCCCCTGGAAAATGAACTTGGTGTTAAAACCCTGGATTGTCAA
AAAGCTCTTATCCCTTTTGAAGAGTTTATTAATGAACCACTGAAAGAGGTTCTAGAAATGCATAAAGATTATACTGTTTT
CAAAGTAGAAACAGAACAAATTCTCTTTTATGACATACCCCTTTTTAGTGTATGCTGTCACAAAGAATTTGGGATTATAT
TATGACAATAAGATTCCCATGTACAGTGAACGAAGAATCACTGTTCTCTACAGCTTAGTTCAAGGACAGCAGTTGAATCC
ATATTTGAGACTCATTGTTAGATGTGACTATATCATAGATGATGCACTTGTCCGGCTAGAGATGATCACTATGGAAAATC
CTGCAGACTTGAAGCAGTTCTATGTGGAATTTGAAGGAGAACAAGGTGAGGGAGGTGTTTCCAAATAATTTTTTCAGCTG
GTTGTGGAGGAAATCTTCAATCCAGATATTGGTGTGTTCACGTACGATGAACTTACAAAATTGTTTTGACTTAATCCA

Alignment

ORF - retro_ggor_1575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 56.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DFKDVTYLTEEKVYEILELCREREDYSPLIR-VIGRVFSSAEALVQSFRKVKQHTKEELKSLQAKDEDKD
          DFKDVTYLTEEKVYEI.ELCREREDYSPL...VIGRVFSSAEALV.SFRK.KQHTKEELKSLQAKDE.K.
Retrocopy DFKDVTYLTEEKVYEITELCREREDYSPLTV<VIGRVFSSAEALVESFRKAKQHTKEELKSLQAKDEEKN

Parental  EDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNA
          E.EK.KAACSAAAMEEDSEASSS..GDSSQGDN.LQKLGPDDVSVD.DAIRRVYTRLLSNEK.E.AFLNA
Retrocopy ENEKAKAACSAAAMEEDSEASSSSTGDSSQGDNSLQKLGPDDVSVDTDAIRRVYTRLLSNEKTEIAFLNA

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

Parental  KYNADQIRRMMETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMVYYAN-VVGGEVDTNHNEEDDE
          KYNADQIRRM.ETFQQL.TYKVISNEFNS.NLVNDDDAIVAASKCLK..YYAN.VVGGEVDTNHNEEDDE
Retrocopy KYNADQIRRMVETFQQLTTYKVISNEFNSQNLVNDDDAIVAASKCLKVIYYAN>VVGGEVDTNHNEEDDE

Parental  EPIPESSELTLQELLGEERRNKKGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFK
          EPIPESSELTLQELL.EERRNKKGP.VDPLE.ELGVKTLDC.K.LIPFEEFINEPL.EVLEM.KDYT.FK
Retrocopy EPIPESSELTLQELLEEERRNKKGP*VDPLENELGVKTLDCQKALIPFEEFINEPLKEVLEMHKDYTVFK

Parental  VETENKFSFMTCP-FILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDAL
          VETE....F...P.F...AVTKNLGLYYDN.I.MYSERRITVLYSLVQGQQLNPYLRL.VR.D.IIDDAL
Retrocopy VETE-QILFYDIP>FLVYAVTKNLGLYYDNKIPMYSERRITVLYSLVQGQQLNPYLRLIVRCDYIIDDAL

Parental  VRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFWFNP
          VRLEMI.MENPADL.KQ.YVEFEGEQG..EGGVSK.FFQLVVEEIFNPDIG.FTYDE.TKLF..NP
Retrocopy VRLEMITMENPADL-KQFYVEFEGEQG--EGGVSK*FFQLVVEEIFNPDIGVFTYDELTKLF*LNP

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	54.81 RPM
SRP007412_cerebellum	0.04 RPM	39.87 RPM
SRP007412_heart	0.00 RPM	12.88 RPM
SRP007412_kidney	0.00 RPM	51.85 RPM
SRP007412_liver	0.00 RPM	43.95 RPM
SRP007412_testis	0.21 RPM	120.07 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1575 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2523
Pan troglodytes	retro_ptro_1468
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,