RetrogeneDB ID: retro_pabe_2110

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:37733940..37734811(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSPPYG00000005232
• Aliases: None
• Description: ubiquitin specific peptidase 12 [Source:HGNC Symbol;Acc:20485]

Sequence

>retro_pabe_2110
AGAAGGAAAATTTTAATGTGCTCAGCAACTTTCTTCCACTGTGTAGCCACACAGAAGGAAAAGGTTGAAGTAATAACTCC
CAAGAAGTTCAAAACAAGATTACAGAAAGAAAATGAGCTTTTCTGCATGCAACAAGATACCCATGGGTTCTTAAATTACC
TACTAAATACAATTGCTGATATTCTATAAGAAGAGAGAAGGCAGGATAAACAAAATGGTCACTTACCAAATGGTAATATT
GATACTGAAAATAACAACAGCACACCAGACCCAATGTAGGTTCATGAAATTTTTCAGAAAACATTAACTAATGAAACCAG
ATGTATTACTTGTGAAACTATAAGAGCAAAGATGAAGATTTTAAAGAACTTCCTGTGATATAGAACAAAATACATCAGTT
ATTCACTGTTTCAGGGTTTTTAGCAACACAGAAACTCTATGAAGTGAATACAGACATTACTGTGAAGAGTGTTGTAGCAA
ACAGGAAGCACACAAATGAATGAAAGTTTAAAAACCACCCATGATTATAGCTCTACATCTGAAAATATTTAAATATATGG
ATTAAATTCACTGATGTACGAAACTTTCTTACTAGGTAGTTTTTCGTTTAGAACTTTGTCTGTGTAACATTTCAGGGGAT
GCAACCAATCCAGACAGAATGCACGACCTTGTTGCTATTATGATTTACTGTGGAAGTGGTCACAGGTGACGCCATTATAT
TGTAACAGTTAAGAATCAAATTTCTGCTTGTCCTTTGATGACACTGTAGAAAAAAATGAATGCACAAATTACTGAAGAAT
TCTATGTATTGACCTCAGATATCACAAAGAACTCAGAGTCTGGTTACATTCTTTTCTATTAGTCTCGGAAC

Alignment

ORF - retro_pabe_2110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.14 %
• Parental protein coverage: 79.46 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KESLLTCLADLFHSIATQKKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQ
          ....L.C.A..FH..ATQK.KV.VI.PKKF.TRL.KENELF...MQQD.H.FLNYLLNTIADIL.EER.Q
Retrocopy RRKILMCSATFFHCVATQKEKVEVITPKKFKTRLQKENELF--CMQQDTHGFLNYLLNTIADIL*EERRQ

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

Parental  CLRGFSNTETLCSEYKYYCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLEL
          C.R.FSNTETL.SEY..YCEEC.SKQEAHK.MKV.K.PMI.ALHLK.FKYMD..H..TKLSY.VVF.LEL
Retrocopy CFRVFSNTETL*SEYRHYCEECCSKQEAHK*MKV*KPPMIIALHLKIFKYMD*IH*CTKLSY*VVFRLEL

Parental  RLFNTSGDATNPDRMYDLVAVVVHCGSGPNRGHYIAIVKSH-DFWLLFDDDIVEK-IDAQAIEEFYGLTS
          .L.N.SGDATNPDRM.DLVA....CGSG....HYI..VK....F.L.F.DD.VEK...AQ..EEFY.LTS
Retrocopy CLCNISGDATNPDRMHDLVAIMIYCGSGHR*RHYIVTVKNQ<NFCLSF-DDTVEK>MNAQITEEFYVLTS

Parental  DISKNSESGYILFYQSRD
          DI.KNSESGYILFY.SR.
Retrocopy DITKNSESGYILFY*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	0.00 RPM	26.59 RPM
SRP007412_cerebellum	0.00 RPM	22.62 RPM
SRP007412_heart	0.00 RPM	13.46 RPM
SRP007412_kidney	0.00 RPM	17.57 RPM
SRP007412_liver	0.00 RPM	12.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2110 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2110 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2328
Pan troglodytes	retro_ptro_1701
Gorilla gorilla	retro_ggor_1767
Macaca mulatta	retro_mmul_937
Callithrix jacchus	retro_cjac_2734

---

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,