RetrogeneDB ID: retro_ptro_1898

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:74188748..74190114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSPTRG00000022722
• Aliases: None
• Description: None

Sequence

>retro_ptro_1898
ATGGCAGATGGCCACTTGGAGCCGGCTGACAGGCGCATCTTCAAAATGGAAGTGGACTACAACGCCACGGTAGATCAGTG
CCTACCCTAGTGTGAGAAGCTGGCCAAGGAAGGAAGACTTCGAGAAGTCATGGAAACCCTTCTCTCTTTGGAAAAACAGA
CTCGTACTGCTTCTGATATGGGGTCAACATCCCAAATCTTAGTTGCAGTAGTGAAGATGTGCTATGAGGCTAAAGAATGG
GATTTACTTAATGAAAATATTACACTTTTGTCCAAAAGGCGGAGTCAGTTAATACAAGCTGTTGCCAAAATGGTTCAATA
GTACTGTATTTATGTTGAGGAAATCACAGACCTTCCTATCAAACTTCAATTAACTGATACTCTATGAATGGTTACCGAAG
GCAAGATTTATGTTGAAATTGAGTGTGCTCGACTGACTAAAACATTAGCAACTATAAAAGAACAAAATGGTGATGTGAAA
GAGGCAGCCTCCGTTTATAGGAGCTACAGGTGGAAACCTATGGATCAATGTAAAAGAAAGAGCAAGTGGAATTTATTTTG
GAGCAAATGAGGCTCTGCCTAGCTGTAAAGGATTATATTCTAACATAAATCATCAGTAAGAAAATTAACACCAAGTTTTT
CCAGGAAGAACACACAGCGAAATTAAAGTTGAAGTACGATAATTTAATGACTCAGCTGGATGAACATGAGGGATCCTATT
TGTTTATTTGTAAGCACTACAGAGCAATATATAATACTCCCTGCATACAGGCAGAAAGTGAAAAATGGCAGCAGGCTATG
AAGAGTGTTGTACCCTATGTTACCCTGGCTCCTTTTGACAATGAACAGTCAGATTTGGTTCACCGAATAAGTGGTGACAA
GAAGTCAGAAGAAATTCCCAAATACAAGGATCTTCTAAAACTTTTTACCACAATGGAGTTGATGCGTTGGTCCACACTTG
TGGAGGACTATGGAATGGAATTAAGAAAAGGTTCCGTTGGCAGTCCTGCAACTGATGCTTTTGGTTCTACAGAGGAAGGC
GAAAAAAGGTGGAAAGATTTGAATAACAGAGTTGTTGAACATAATATTAGAATAATGGCCAAGTATTATACTCGGATGAC
AACGAAAAGGATGGTACAGCTTCTGGATCTATCTGTTGATGAGTCCGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAGA
CCATATTTGCTAAAGTAGACAGATTAGCAGGAATTAACAACTTCCAGAGACCCAAGGATCCAAATAATTTATGAAATGGC
TGGTCTCAGAAACTGAACTCATTAATGTCTCTGGTTAACAAAACTACCATCTCATAGCTAAAGAGGAGATGATACATAAT
CTACAA

Alignment

ORF - retro_ptro_1898 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
          MADG..E.AD.RI.KMEVDY.ATVDQ.LP.C.KLAKEGRL.EV.ETLLSLEKQTRTASDM.STS.ILVAV
Retrocopy MADGHLEPADRRIFKMEVDYNATVDQCLP*CEKLAKEGRLREVMETLLSLEKQTRTASDMGSTSQILVAV

Parental  VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
          VKMCYEAKEWDLLNENI.LLSKRRSQL.QAVAKMVQ..C.YVEEITDLPIKL.L.DTL.MVTEGKIYVEI
Retrocopy VKMCYEAKEWDLLNENITLLSKRRSQLIQAVAKMVQ*YCIYVEEITDLPIKLQLTDTL*MVTEGKIYVEI

Parental  ERARLTKTLATIKEQNGDVKEAASILQ-ELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKI
          E.ARLTKTLATIKEQNGDVKEAAS....ELQVETYGSM.KKE.VEFILEQMRLCLAVKDYI.T.IISKKI
Retrocopy ECARLTKTLATIKEQNGDVKEAASVYR<ELQVETYGSM*KKEQVEFILEQMRLCLAVKDYILT*IISKKI

Parental  NTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPF
          NTKFFQEE.T.KLKLKY.NLM.QLD.HEGSYL.ICKHYRAIY.TPCIQAESEKWQQA.KSVV.YV.LAPF
Retrocopy NTKFFQEEHTAKLKLKYDNLMTQLDEHEGSYLFICKHYRAIYNTPCIQAESEKWQQAMKSVVPYVTLAPF

Parental  DNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEK
          DNEQSDLVHRISGDKK.EEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGS..SPATD.FGSTEEGEK
Retrocopy DNEQSDLVHRISGDKKSEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSVGSPATDAFGSTEEGEK

Parental  RWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPK
          RWKDL.NRVVEHNIRIMAKYYTR.T.KRM.QLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGI.NFQRPK
Retrocopy RWKDLNNRVVEHNIRIMAKYYTRMTTKRMVQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGINNFQRPK

Parental  DPNNLLNDWSQKLNSLMSLVNKTT-HLIAKEEMIHNLQ
          DPNNL.N.WSQKLNSLMSLVNKTT.HLIAKEEMIHNLQ
Retrocopy DPNNL*NGWSQKLNSLMSLVNKTT<HLIAKEEMIHNLQ

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	0.04 RPM	15.87 RPM
SRP007412_cerebellum	0.00 RPM	17.96 RPM
SRP007412_heart	0.00 RPM	18.27 RPM
SRP007412_kidney	0.00 RPM	15.87 RPM
SRP007412_liver	0.00 RPM	26.68 RPM
SRP007412_testis	0.32 RPM	41.63 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1898 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1898 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1898 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2801
Gorilla gorilla	retro_ggor_1947
Callithrix jacchus	retro_cjac_1400

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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,