RetrogeneDB ID: retro_nleu_1569

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397299.1:19047914..19049084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC7
• Ensembl ID: ENSNLEG00000011230
• Aliases: None
• Description: None

Sequence

>retro_nleu_1569
TTCAAGGAACAAGGAAATGCGTATTATGCCAAGAAATATTACAATGACGCTTGTAATTATTATACAAAAGCCATAGGCAT
ATGTCCTAAAAATGCTAGCTACTACAGTAATCAAGCAGCCACATTGATTATGCTTGGAAGGTTCCAGGAAGCTCTTGGAG
ATGCACACCAGTCACTGAGATTGGATGGCAGTTTTGTTCAGGGACATCCAGGAGAGGGCAAGTGCCCCCCTCTCTCTAGA
GAATGCCATGGCCACATGTCAGTTTCCAGAGAGCCCTAGAACTGGATCATAAAAATGCTCAGGAATAACAGGAGTTCAAG
AATGCTAATTCAATCATGGAATATGAGAAGTTAGCAAAAATAGATTTTGAGAAGCATATTAGGAAGGTTGTTCTCTGCAA
GGACTGTGCCCTAGCACTTGCCCCTGCCTGCCATTGCTTCAAAATCCTCAAAGCGGAATATTCAGTAATGCTGGGTCATT
ATCCAGAAGCACAATCTGTGGCCAGTGACATTTTACAAATGGAGTCCACCAATGCAGATCCTCTGTATGTATAAGGTCTT
TGCCTTTATTAAGATTGTGTTGAGAAGGCAGTTCAGGTTTTTGTATAGGCTCTCAGGATGGCTCCATGAGAGGGCCTGCG
TTGCTTGCAGAAATCCCAAAGCACTCAAAGCAAAGAAAGAAGACAGAAATAAAGCATTTAAGGGAGGAAATTACAAGCTA
GCATACGAACTGTACACATGAGCCCTGGGGATAAACCCCAACAGTATAAAAACAAATGCTAAACTCTACTATAATCAGGT
TATGGTTAATTCTAAGCTTAGGAAACTAGATAATGCAATACAAGACTGCACAAATACAGTGAAGCTCAATGACACCTATT
TAAAAGCCTGCTTGAGAAGAGCTCAGTGTTACATGAACACCAAACAGTAAGAAGAAGCAGTGCACAATTATGAAAAAGTG
TATCAGACAGAGAAAACAAAAGAACACAAACAGCTCCTAAAAAATGCACAGCTGAAACTGAAGAAGAGTAAGAAGAAAGA
TTACTACAAGATTCTGGGAGTGGACAATAATGTCTCTGAGGACGAGACCAAGAAAGCTTATCACAAATGGGCCTTGATGC
ACCATCCACATTGGCACAGTGGAGGCAGTGCTGAGGTTCAGAAGGAGGAG

Alignment

ORF - retro_nleu_1569 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.74 %
• Parental protein coverage: 84.01 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FKEQGNAYYAKKDYNEAYNYYTKAIDMCPKNASYYGNRAATLMMLGRFREALGDAQQSVRLDDSFVRGH-
          FKEQGNAYYAKK.YN.A.NYYTKAI..CPKNASYY.N.AATL.MLGRF.EALGDA.QS.RLD.SFV.GH.
Retrocopy FKEQGNAYYAKKYYNDACNYYTKAIGICPKNASYYSNQAATLIMLGRFQEALGDAHQSLRLDGSFVQGH<

Parental  LREGKCHLSLGNAMAACRSFQRALELDHKNAQAQQEFKNANAVMEYEKIAETDFEKRDFRKVVFCMDRAL
          .R.G....SL........SFQRALELDHKNAQ..QEFKNAN..MEYEK.A..DFEK...RKVV.C.D.AL
Retrocopy SRRGQVPPSL*RMPWPHVSFQRALELDHKNAQE*QEFKNANSIMEYEKLAKIDFEKH-IRKVVLCKDCAL

Parental  EFAPACHRFKILKAECLAMLGRYPEAQSVASDILRMDSTNADALYVRGLCLYYEDCIEKAVQFFVQALRM
          ..APACH.FKILKAE...MLG.YPEAQSVASDIL.M.STNAD.LYV.GLCL.Y.DC.EKAVQ.FV.ALRM
Retrocopy ALAPACHCFKILKAEYSVMLGHYPEAQSVASDILQMESTNADPLYV*GLCL-Y*DCVEKAVQVFV*ALRM

Parental  APDHEKACIACRNAKALKAK-KEDGNKAFKEGNYKLAYELYTEALGIDPNNIKTNAKLYCNRGTVNSKLR
          AP.....C...........K.KED.NKAFK.GNYKLAYELYT.ALGI.PN.IKTNAKLY.N...VNSKLR
Retrocopy AP*EGLRCL--QKSQSTQSK>KEDRNKAFKGGNYKLAYELYT*ALGINPNSIKTNAKLYYNQVMVNSKLR

Parental  KLDDAIEDCTNAVKLDDTYIKAYLRRAQCYMDTEQYEEAVRDYEKVYQTEKTKEHKQLLKNAQLELKKSK
          KLD.AI.DCTN.VKL.DTY.KA.LRRAQCYM.T.Q.EEAV..YEKVYQTEKTKEHKQLLKNAQL.LKKSK
Retrocopy KLDNAIQDCTNTVKLNDTYLKACLRRAQCYMNTKQ*EEAVHNYEKVYQTEKTKEHKQLLKNAQLKLKKSK

Parental  RKDYYKILGVDKNASEDEIKKAYRKRALMHHPDRHSGASAEVQKEE
          .KDYYKILGVD.N.SEDE.KKAY.K.ALMHHP..HSG.SAEVQKEE
Retrocopy KKDYYKILGVDNNVSEDETKKAYHKWALMHHPHWHSGGSAEVQKEE

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_1569 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.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015749	1 retrocopy	retro_cfam_451,
Callithrix jacchus	ENSCJAG00000035699	2 retrocopies	retro_cjac_2381, retro_cjac_2475,
Homo sapiens	ENSG00000168259	1 retrocopy	retro_hsap_3524,
Gorilla gorilla	ENSGGOG00000010230	2 retrocopies	retro_ggor_2382, retro_ggor_396,
Myotis lucifugus	ENSMLUG00000011968	2 retrocopies	retro_mluc_1232, retro_mluc_1527,
Macaca mulatta	ENSMMUG00000016118	3 retrocopies	retro_mmul_1084, retro_mmul_1854, retro_mmul_501,
Nomascus leucogenys	ENSNLEG00000011230	2 retrocopies	retro_nleu_1569 , retro_nleu_490,
Pongo abelii	ENSPPYG00000008402	2 retrocopies	retro_pabe_2911, retro_pabe_317,
Pan troglodytes	ENSPTRG00000009188	2 retrocopies	retro_ptro_2393, retro_ptro_304,