RetrogeneDB ID: retro_pabe_2223

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 3:72748788..72750156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSPPYG00000008565
• Aliases: None
• Description: 26S proteasome non-ATPase regulatory subunit 12 [Source:RefSeq peptide;Acc:NP_001125501]

Sequence

>retro_pabe_2223
ATGGTGGATGGCCACTTGGAACGGGCTGTCAGGCGCATCGTCAAAATGGAAGTGGACTATAGCGCCACAGTGGATCAGTG
CCTACCCGAGTGTGAGAAGCTGGCCAAGGAAGGAAGACTTCAAGAAGTCACTGAAACCCTTCTCTCTTTGGAAAAACAGA
CTCATTCCGCTTCTGATATGGCGTCTACATCCCAAGTCTTAGTTGCAGTAGTGAAGATGTGTTATGAGGCTAAAGAATGG
GATTTACTTAATGAAAATATTACGCTTTTGTCCAAAAGGCAGAGTCAGTTAATATAAGCTGTTGCCAAAATGGTTCAATA
GTACTGTATTTATGTTGAGGAAATCACAGACCTTCCTATCAAACTTCAATTAATTGATACTCTATGAATGGTTACCAAAG
GCAAGATTTATGTTGAAACTGAGTATCCTCGACTGACTAAAACATTAGCAACTATAAAATAACAAAATGGTGATGTGAAA
GAGGCAGCCTCCGTTTTATAGGAGTTACAGGTGGAAACCTATGGGTCAATGTAAAAGAAAGAGCAAGTGGAATTTATTTT
GGAGCAAATGAGGCTCTGCCTAGCTGTAAAGGATTACATTCGAACATAAATCATCAGTAAGAAAATTAACACCAAGTTTT
TCCAGGAAGAAAATACAGAGAAATTAAAGTTGAAGTATGATAATTTAATGATTCAGCTGGATCAACATCAGAGATCCTAT
TTGTTCATTTGTAAACACTACAGAGCAATATATAATACTCCCTGTATACAGGCAGACAGTGAAAAATGGCAGCAGGCTAT
GAAGCGTGTTGTACCCTATGTTACCCTAGCTCCTTTTGACAATGAACAGTCAGATTTGGTTCACTGAGTAAGTGGTGACA
AGAAGTCAGAACAAACTCCCAAATACAAGGATCTTCTAAGGCTTTTTACCACAATGGAGTTGATGTGTTAGTCCACACTT
GTGGAGGACTATGCAATGGAATTAAGAAAAGGTTCCCTTGAGAGTCCTGCAACTGATGTTTTTGGTTCTACAGAGGAAGG
CAAAAAAAGGTGGAAAGACTTGAAGAACAGAGTTGTTGAACATAATATTAAAATAATGGCCAAGTATTATACTCGGATAA
CAATGAAAAGGATGGTACAGCTTCTGGATCTATCTGTTGATGAGTCCGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAG
ACCATCTTTGCTAAAGTAGACAGATTAGCAGGAATTAACAACTTCCAGAGACCCAAGGATCCAAATAATTTATTAAATGA
CCCGTCTCAGAAACTGAACTCATTAATGTCTCTGGTTAACAAAACTACACATCTCGTAGCCAAAGAGGAGATGATACATA
ATCCACAA

Alignment

ORF - retro_pabe_2223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
          M.DG..ERA..RIVKMEVDYSATVDQ.LPEC.KLAKEGRLQEV.ETLLSLEKQT..ASDM.STS..LVAV
Retrocopy MVDGHLERAVRRIVKMEVDYSATVDQCLPECEKLAKEGRLQEVTETLLSLEKQTHSASDMASTSQVLVAV

Parental  VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
          VKMCYEAKEWDLLNENI.LLSKR.SQL..AVAKMVQ..C.YVEEITDLPIKL.LIDTL.MVT.GKIYVE.
Retrocopy VKMCYEAKEWDLLNENITLLSKRQSQLI*AVAKMVQ*YCIYVEEITDLPIKLQLIDTL*MVTKGKIYVET

Parental  ERARLTKTLATIKEQNGDVKEAASILQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKIN
          E..RLTKTLATIK.QNGDVKEAAS.L.ELQVETYGSM.KKE.VEFILEQMRLCLAVKDYIRT.IISKKIN
Retrocopy EYPRLTKTLATIK*QNGDVKEAASVL*ELQVETYGSM*KKEQVEFILEQMRLCLAVKDYIRT*IISKKIN

Parental  TKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPFD
          TKFFQEENTEKLKLKY.NLMIQLDQH..SYL.ICKHYRAIY.TPCIQA.SEKWQQA.K.VV.YV.LAPFD
Retrocopy TKFFQEENTEKLKLKYDNLMIQLDQHQRSYLFICKHYRAIYNTPCIQADSEKWQQAMKRVVPYVTLAPFD

Parental  NEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEKR
          NEQSDLVH..SGDKK.E..PKYKDLL.LFTTMELM..STLVEDY.MELRKGSLESPATDVFGSTEEG.KR
Retrocopy NEQSDLVH*VSGDKKSEQTPKYKDLLRLFTTMELMC*STLVEDYAMELRKGSLESPATDVFGSTEEGKKR

Parental  WKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPKD
          WKDLKNRVVEHNI.IMAKYYTRITMKRM.QLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGI.NFQRPKD
Retrocopy WKDLKNRVVEHNIKIMAKYYTRITMKRMVQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGINNFQRPKD

Parental  PNNLLNDWSQKLNSLMSLVNKTTHLIAKEEMIHNLQ
          PNNLLND.SQKLNSLMSLVNKTTHL.AKEEMIHN.Q
Retrocopy PNNLLNDPSQKLNSLMSLVNKTTHLVAKEEMIHNPQ

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	30.35 RPM
SRP007412_cerebellum	0.00 RPM	40.37 RPM
SRP007412_heart	0.00 RPM	15.59 RPM
SRP007412_kidney	0.03 RPM	19.26 RPM
SRP007412_liver	0.00 RPM	24.73 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2223 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008691	2 retrocopies	retro_cjac_1400, retro_cjac_2793,
Homo sapiens	ENSG00000197170	1 retrocopy	retro_hsap_2801,
Gorilla gorilla	ENSGGOG00000014761	1 retrocopy	retro_ggor_1947,
Loxodonta africana	ENSLAFG00000010876	1 retrocopy	retro_lafr_467,
Nomascus leucogenys	ENSNLEG00000001265	1 retrocopy	retro_nleu_1541,
Pongo abelii	ENSPPYG00000008565	1 retrocopy	retro_pabe_2223 ,
Pan troglodytes	ENSPTRG00000022722	1 retrocopy	retro_ptro_1898,
Tupaia belangeri	ENSTBEG00000014760	1 retrocopy	retro_tbel_443,
Tarsius syrichta	ENSTSYG00000013154	1 retrocopy	retro_tsyr_1670,