RetrogeneDB ID: retro_ggor_1767

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:35625175..35626044(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP46
• Ensembl ID: ENSGGOG00000017197
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G3RLX0]

Sequence

>retro_ggor_1767
AGAAGGAAAATTTTAATGTGCTCAGCAACTTTCTTCCACTGTGTAGCCACACAGAAGGAAAAGGTTGAAGTAATATCTCC
CGAGAAGTTCAAAACAAGATTACAGAAAGAAAATGAGTTTTTCTGCATGCAACAAGATACCCATGGGTTCTTAAATTACC
TACTAAATACAATTGCTGATATTCTATAAGAAGAGAGAAGGCAGGATAAACAAAATGGTCACTTACCAAATGGTAATATT
GATACTGAAAATAACAACAGCACACCAGACCCAATGTAGGTTCACGAAATTTTTCAGAAAACATTAACTAATGAAACCAG
ATGTATTACTTGTGAAACTGTAAGAGCAAAGATGAAGATTTTAAAGAACTTCCTGTGATATAGAATAAAATGCATCAGTT
ATTCACTGTTTAAGGGTTTTTAGCAACGCAGAAACTCTATGAAGTGAATACAGACATTACTGTGAAGAGTGTTGTAGCAA
ATAGGAAGCACACAAATGAATGAAAGTTTAAAAACCACCCATGATTAGAGCTCTACATCTGAAAATATTTAAATATATGG
ATTAAATTCACTGATGTACGAAACTTTCTTACTAGGTAGTTTTTCGTTTAGAACTTTGTCTGTGTAACACTTCAGGGGAT
GCAACCAATCCAGACAGAATGCACGACCTTGTTGCTATTATGATTTACTGTGGAAGTGGTCACAGGTGAGGCCATTATAT
TGTAATAGTTAAGAATCAAGATTTCTGCTTGTCCTTTGATGATACTGTAGAAAAAAATGAATGCACAAATTACTGAAGAA
TTCTATGTATTGACCTCAGATATTGCAAAGAACTCAGAGTCTGGTTACGTTCTTTTCTATTAGTCTCGG

Alignment

ORF - retro_ggor_1767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.51 %
• Parental protein coverage: 79.84 %
• Number of stop codons detected: 12
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KENLLTCLADLFHSIATQKKKVGVIPPKKFISRLRKENDLFDNYMQQDAHEFLNYLLNTIADILQEEKKQ
          ....L.C.A..FH..ATQK.KV.VI.P.KF..RL.KEN..F...MQQD.H.FLNYLLNTIADIL.EE..Q
Retrocopy RRKILMCSATFFHCVATQKEKVEVISPEKFKTRLQKENEFF--CMQQDTHGFLNYLLNTIADIL*EERRQ

Parental  EKQNGKLKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETV-SSKDEDFLDLSV-DVEQNTSITH
          .KQNG.L.NGN......N..P....VHEIFQ.TLTNETRC..CETV..SKDEDF..L.V.D.E.N.S..H
Retrocopy DKQNGHLPNGNIDTENNNSTPDPM*VHEIFQKTLTNETRCITCETV<KSKDEDFKELPV<DIE*NASVIH

Parental  CLRDFSNTETLCSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLKRFKYMEQLHRYTKLSYRVVFPLEL
          CLR.FSN.ETL.SE...YCE.CCSK.EA.K.M.V.K.PMI.ALHLK.FKYM...H..TKLSY.VVF.LEL
Retrocopy CLRVFSNAETL*SEYRHYCEECCSK*EAHK*MKV*KPPMIRALHLKIFKYMD*IH*CTKLSY*VVFRLEL

Parental  RLFNTSSDAVNLDRMYDLVAVVVHCGSGPNRGHYITIVKSHGFWLLFDDDIVEK-IDAQAIEEFYGLTSD
          .L.NTS.DA.N.DRM.DLVA....CGSG...GHYI.IVK...F.L.F.DD.VEK...AQ..EEFY.LTSD
Retrocopy CLCNTSGDATNPDRMHDLVAIMIYCGSGHR*GHYIVIVKNQDFCLSF-DDTVEK>MNAQITEEFYVLTSD

Parental  ISKNSESGYILFYQSR
          I.KNSESGY.LFY.SR
Retrocopy IAKNSESGYVLFY*SR

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	52.17 RPM
SRP007412_cerebellum	0.16 RPM	41.33 RPM
SRP007412_heart	0.00 RPM	10.38 RPM
SRP007412_kidney	0.04 RPM	25.64 RPM
SRP007412_liver	0.05 RPM	6.86 RPM
SRP007412_testis	0.10 RPM	26.31 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_1767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1767 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2328
Pan troglodytes	retro_ptro_1701
Pongo abelii	retro_pabe_2110
Macaca mulatta	retro_mmul_937
Callithrix jacchus	retro_cjac_2734

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007660	1 retrocopy	retro_cpor_1157,
Gorilla gorilla	ENSGGOG00000017197	3 retrocopies	retro_ggor_1767 , retro_ggor_2223, retro_ggor_2937,