RetrogeneDB ID: retro_nleu_1541

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397298.1:4935866..4937229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD12
• Ensembl ID: ENSNLEG00000001265
• Aliases: None
• Description: None

Sequence

>retro_nleu_1541
ATGGCGGACGGCTGCTTGGAGTGAATTGACGGGCGCATCTTCAAAATGGAAGTGGACTACAACGCCACGGTGGATCAGTG
CCTACCCGAGTGTGAGAAGCTGGACAAGGAAGGAAGACTTCAAGAAGTCATGGAAACCCTTCTCTCTTTGGAAAAACAGA
CTCGTACTGCTTCTGATATGGTGTCAACATCCCAAATCTTAGTTGCAGTAGTGAAGATGTGCTATGAGGCTAAAGAATGG
GATTTACTTAATGAAAATATTATGCTTTTGTCCAAAAGGCGGACTCAGTTAATACAAGCTGTTGCCAAAATGGTTCAATA
GTACTGTATTTATGTTGAGGAAATCACAGACCTTCCTACCAAACTTCAATTAATTGATATTCTATGAATGGTTACTGAAG
GCAAGATTTATGTTGAAATTGAGTGTGCTCGACTGACTAAAACCTTAGCAACTATAAAAGAACAAAATGGTGATGTGAAA
GAGGCAGCCTCTGTTTACAGGAGCTACAGGTGGAAACCTATGGGTCAATGTAAAAGAAAGAGCAAGTGGAATTTATTTTG
GAGCAAATGAGGCTCTGCTTAGCTGTAAAGGATTACATTCAAACATAAATCATGAGTAAGAAAATTAACACCAAGTTTTT
CCAGGAAGAAGATACAGAGAAATTAAAGTTGAAGTACGATAATTTAATGACTCAGCTGGATCAACATGAGGGATCCTATT
TGTTTATTTGTAAGCACTACAGAGCAATATATAATACTCCCTGTATACAGGCAGAAAGTGAAAAATGGCAGCAGGCTATG
AAGAGTGTTGTACCCTATGTTACCCTGGCTCCTTTTGACAATGAACAGTCAGATTTGGTTCACTGAATAAGTGGTGACAA
GAAGTCAGAAGAAATTCCCAAATACAAGGATCTTCTAAAGCTTTTTACCACAATGGAGTTGATGCGTTGGTCCACACTTG
TGGAGGACTGTGGAATGGAATTAAGAAAAGGTTCCCTTGAGAGTCCTGCAACTGATGTTTTTGATTCTACAGAGGAAGGT
GAAAAAAGGTGGAAAGACTTGAATAACAGAGTTGTTGAACATAATATTAGAATAATGGCCAAGTATTATACTAGGATAAC
AATGAAAAGTATGGTACAGCTTCTGGGTCTATCTGTTGATGAGTCCGAAGCCTTTCTCTCAAATCTAGTAGTTAACAAGA
CCATCTTTGCTAAAGTAGACAGATCAGCAGGAATTAACAACTTCCAGAGACCCAAGGATCCAAATAATTTATTAAATGAC
TGGTCTCAGAAACTGAACTCATTAATGTCTCTGATTAACAAAACTACACATCTCATACCAAAGAGAAGATGATACATAAT
CTA

Alignment

ORF - retro_nleu_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.06 %
• Parental protein coverage: 99.78 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADGGSERADGRIVKMEVDYSATVDQRLPECAKLAKEGRLQEVIETLLSLEKQTRTASDMVSTSRILVAV
          MADG..E..DGRI.KMEVDY.ATVDQ.LPEC.KL.KEGRLQEV.ETLLSLEKQTRTASDMVSTS.ILVAV
Retrocopy MADGCLE*IDGRIFKMEVDYNATVDQCLPECEKLDKEGRLQEVMETLLSLEKQTRTASDMVSTSQILVAV

Parental  VKMCYEAKEWDLLNENIMLLSKRRSQLKQAVAKMVQQCCTYVEEITDLPIKLRLIDTLRMVTEGKIYVEI
          VKMCYEAKEWDLLNENIMLLSKRR.QL.QAVAKMVQ..C.YVEEITDLP.KL.LID.L.MVTEGKIYVEI
Retrocopy VKMCYEAKEWDLLNENIMLLSKRRTQLIQAVAKMVQ*YCIYVEEITDLPTKLQLIDIL*MVTEGKIYVEI

Parental  ERARLTKTLATIKEQNGDVKEAASI-LQELQVETYGSMEKKERVEFILEQMRLCLAVKDYIRTQIISKKI
          E.ARLTKTLATIKEQNGDVKEAAS..LQELQVETYGSM.KKE.VEFILEQMRLCLAVKDYI.T.I.SKKI
Retrocopy ECARLTKTLATIKEQNGDVKEAASV<LQELQVETYGSM*KKEQVEFILEQMRLCLAVKDYIQT*IMSKKI

Parental  NTKFFQEENTEKLKLKYYNLMIQLDQHEGSYLSICKHYRAIYDTPCIQAESEKWQQALKSVVLYVILAPF
          NTKFFQEE.TEKLKLKY.NLM.QLDQHEGSYL.ICKHYRAIY.TPCIQAESEKWQQA.KSVV.YV.LAPF
Retrocopy NTKFFQEEDTEKLKLKYDNLMTQLDQHEGSYLFICKHYRAIYNTPCIQAESEKWQQAMKSVVPYVTLAPF

Parental  DNEQSDLVHRISGDKKLEEIPKYKDLLKLFTTMELMRWSTLVEDYGMELRKGSLESPATDVFGSTEEGEK
          DNEQSDLVH.ISGDKK.EEIPKYKDLLKLFTTMELMRWSTLVED.GMELRKGSLESPATDVF.STEEGEK
Retrocopy DNEQSDLVH*ISGDKKSEEIPKYKDLLKLFTTMELMRWSTLVEDCGMELRKGSLESPATDVFDSTEEGEK

Parental  RWKDLKNRVVEHNIRIMAKYYTRITMKRMAQLLDLSVDESEAFLSNLVVNKTIFAKVDRLAGIINFQRPK
          RWKDL.NRVVEHNIRIMAKYYTRITMK.M.QLL.LSVDESEAFLSNLVVNKTIFAKVDR.AGI.NFQRPK
Retrocopy RWKDLNNRVVEHNIRIMAKYYTRITMKSMVQLLGLSVDESEAFLSNLVVNKTIFAKVDRSAGINNFQRPK

Parental  DPNNLLNDWSQKLNSLMSLVNKTTHLI-AKEEMIHNL
          DPNNLLNDWSQKLNSLMSL.NKTTHLI..KE.MIHNL
Retrocopy DPNNLLNDWSQKLNSLMSLINKTTHLI<TKEKMIHNL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1541 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

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,