RetrogeneDB ID: retro_ptro_1701

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:152378730..152379602(-)
• Located in intron of: ENSPTRG00000029184

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSPTRG00000005727
• Aliases: USP12, USP12P1
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:H2Q7B8]

Sequence

>retro_ptro_1701
AGAAGGAAAATTTTAATGTGCTCAGCAACTTTCTTCCACTGTGTAGCCACACAGAAGGAAAAGGTTGAAGTAATATCTCC
CGAGAAGTTCAAAACAAGATTACAGAAAGAAAATGAGTTTTTCTGCATGCAACAAGATACCCATGAGTTCTTAAATTACC
TACTAAATACAATTGCTGATATTCTATAAGAAGAGAGAAGGCAGGATAAACAAAATGGTCACTTACCAAATGGTAATATT
GATAATGAAAATAACAACAGCACACCAGACCCAATGTAGGTTCATGAAATTTTTCAGAAAACATTAACTAATGAAACCAG
ATGTATTACTTGTGAAACTATAAGAGCAAAGATGAAGATTTTAAAGAACTTCCTGTGATATAGAACAAAATACATCAGTT
ATTCACTGTTTAAGGGTTTTTAGCAACACAGAAACTCTATGAAGTGAATACAGACATTACTGTGAAGAGTGTTGTAGCAA
ATAGGAAGCACACAAATGAATGAAAGTTTAAAAACCACCCATGATTAGAGCTCTACATCTGAAAATATTTAAATATATGG
ATTAAATTCACTGATGTACGAAACTTTCTTACTAGGTAGTTTTTCATTTAGAACTTTGTCTGTGTAACACTTCAGGGGGT
GCAACCAATCCAGACAGAATGCACGACCTTGTTGCTATTATGATTTACTGCGGAAGTGGTCACAGGTGAGGCCATTATAT
TGTAATAGTTAAGAATCAAGATTTCTGCTTGTCCTTTGATGACACTGTAGAAAAAAATGAATGCACAAATTACTGAAGAA
TTCTATGTATTGACCTCAGATATTGCAAAGAACTCAGAGTCTGGTTACGTTCTTTTCTATTAGTCTCGGAAC

Alignment

ORF - retro_ptro_1701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.05 %
• Parental protein coverage: 79.46 %
• Number of stop codons detected: 11
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQ
          ....L.C.A..FH..ATQK.KV.VI.P.KF.TRL.KENE.F...MQQD.HEFLNYLLNTIADIL.EER.Q
Retrocopy RRKILMCSATFFHCVATQKEKVEVISPEKFKTRLQKENEFF--CMQQDTHEFLNYLLNTIADIL*EERRQ

Parental  EKQNGRLPNGNIDNENNNSTPDPTWVHEIFQGTLTNETRCLTCETI-SSKDEDFLDLSV-DVEQNTSITH
          .KQNG.LPNGNIDNENNNSTPDP..VHEIFQ.TLTNETRC.TCETI..SKDEDF..L.V.D.EQNTS..H
Retrocopy DKQNGHLPNGNIDNENNNSTPDPM*VHEIFQKTLTNETRCITCETI<KSKDEDFKELPV<DIEQNTSVIH

Parental  CLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLEL
          CLR.FSNTETL.SEY..YCEEC.SK.EAHK.MKV.K.PMI.ALHLK.FKYMD..H..TKLSY.VVF.LEL
Retrocopy CLRVFSNTETL*SEYRHYCEECCSK*EAHK*MKV*KPPMIRALHLKIFKYMD*IH*CTKLSY*VVFHLEL

Parental  RLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEK-IDAQAIEEFYGLTSD
          .L.NTSG.ATNPDRM.DLVA....CGSG...GHYI.IVK..DF.L.F.DD.VEK...AQ..EEFY.LTSD
Retrocopy CLCNTSGGATNPDRMHDLVAIMIYCGSGHR*GHYIVIVKNQDFCLSF-DDTVEK>MNAQITEEFYVLTSD

Parental  ISKNSESGYILFYQSRD
          I.KNSESGY.LFY.SR.
Retrocopy IAKNSESGYVLFY*SRN

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	0.05 RPM	42.08 RPM
SRP007412_cerebellum	0.04 RPM	43.88 RPM
SRP007412_heart	0.00 RPM	34.10 RPM
SRP007412_kidney	0.03 RPM	42.03 RPM
SRP007412_liver	0.03 RPM	32.83 RPM
SRP007412_testis	0.00 RPM	40.47 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1701 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1701 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2328
Gorilla gorilla	retro_ggor_1767
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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995, retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701 , retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,