RetrogeneDB ID: retro_nleu_1006

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397278.1:8603487..8604842(-)
• Located in intron of: ENSNLEG00000009583

Retrocopy information

• Ensembl ID: ENSNLEG00000009607
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DLST
• Ensembl ID: ENSNLEG00000016330
• Aliases: None
• Description: None

Sequence

>retro_nleu_1006
ATGCTGTCCCGGTCCCGCTGTGTGTCCCGGGCGTTCAGACGCTCACTCTCCACCTTCCAGAAGGGGAACTGCCCTCTAGG
AAGATGTTCCCTGCCTGGGGTCTCTTTATGCCAGGGACCAGGTTACCCTAACAGCAGGAAGGTTGTCATTAACAGTGTCT
TCAGTGTTCGCTTCTTCAGAACTACAGCTGTATGCAAGGATGACTTGGTTACAGTCAAAACCCCAGCGTTTGCAGAATCT
GTCACAGAGGAAGATGTCGGGTGGGAGAAAGCTGTTGGAGACACAGTTGCAGAAGATGAAGTGGTTTGTGAGATTGAAAC
TGCCAAGACATTGGTGCAGGTTCCATCATCAGCAAATGGTGTGATTGAAGCTCTTTTGGTACCTGATGGGGGAAAAGTCA
AAGGAGGCACTCTGCTTTTCACACTCAGGAAAACTGGTGCTGCTCCTGCTAAGGCGAAGCCAGCTGAAACTCTGCTGCTG
CAGCCCCAAAAGCAGAACCTATAGCAGCGGTAGTTCCTCCCCCTGCAGCACCCATACCCACTCAGATGCCACCAGTGCCC
TCACCCTCACAACCTCCTTCTAGCAAATCTGTGTCTGCAGTAAAACCTACTGTTGTTCCACCACTAGCTGAGCCAGGAGC
TGGCAAAGGTCTGCATTCAGAACATCGGGAGAAAAAGAACAGGATGTGGCAGTGCATTGCTCAGCGTCTGAAGAAGGCCC
AGAATACATGTGCATTGCTGACAACTTTTAATGAGATTGACATGAGTAACATCCAGGAGATGAGGGCTCGGCACAAAGAG
GCTTTTTTGAAGAAACATAACCTCAAACTAGGCTTCATGTCGGCATTTGTGAAGGCCTTAGCCTTTGCCTTGCAGGAACA
GCCTGTTGTAAATGCAGTGATTGACAATATAACCAAAGAGGTGATATATAGGGATTATATTGACATCAGTGTTGCAGTGG
CCACCCCACAGGGTCTGGTGGTTCCAGTCATCAGGAATTTGGAAGCTATGAATTATGCAGATATTGAACAGACAATCACT
GAACTGGGGGAAAAGGCCTGAAAGAATGAACTTGCCATCGAAGATATGGATGGCGGTACCTTCACCATTAGCAATGGAGG
CGTTTTTGGCTTGCTCTTTGGAACACCCATTATCAACCCCCCTCAGTCTGCCATCCTGGGGATGCATGGCATCTTTGACA
GGCCAGTGGCTATAGGAGGCAAGGTAGAGGTGCGGCCCATGATGTATGTGGCACTGACCTATGATCACCGGCTGACTGAT
GGCAGAGAGGCTGTGACTTTCCTTGGCAAAATCAAGGCAGCGGTAGAGGATCCCAGAGTCGTCCTCCTGGATCTT

Alignment

ORF - retro_nleu_1006 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.75 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSRSRCVSRAFSRSLSAFQKGNCPLGRRSLPGVSLCQGPGYPNSRKVVINNSVFNVRFFRTTAVCKDDL
          MLSRSRCVSRAF.RSLS.FQKGNCPLGR.SLPGVSLCQGPGYPNSRKVVIN.SVF.VRFFRTTAVCKDDL
Retrocopy MLSRSRCVSRAFRRSLSTFQKGNCPLGRCSLPGVSLCQGPGYPNSRKVVIN-SVFSVRFFRTTAVCKDDL

Parental  VTVKTPAFAESVTEGDVRWEKAVGDTVAEDEVVCEIETDKTSVQVPSPANGVIEALLVPDGGKVEGGTPL
          VTVKTPAFAESVTE.DV.WEKAVGDTVAEDEVVCEIET.KT.VQVPS.ANGVIEALLVPDGGKV.GGT.L
Retrocopy VTVKTPAFAESVTEEDVGWEKAVGDTVAEDEVVCEIETAKTLVQVPSSANGVIEALLVPDGGKVKGGTLL

Parental  FTLRKTGAAPAKAKPAEA-PAAAAPKAEPTAAAVPPPAAPIPTQMPLVPSPSQPPSGKPVSAVKPTAALP
          FTLRKTGAAPAKAKPAE...AAAAPKAEP.AA.VPPPAAPIPTQMP.VPSPSQPPS.K.VSAVKPT...P
Retrocopy FTLRKTGAAPAKAKPAET<SAAAAPKAEPIAAVVPPPAAPIPTQMPPVPSPSQPPSSKSVSAVKPTVVPP

Parental  LAEPGAGKGLRSEHREKMNRMRQRIAQRLKEAQNTCAMLTTFNEIDMSNIQEMRARHKEAFLKKHNLKLG
          LAEPGAGKGL.SEHREK.NRM.Q.IAQRLK.AQNTCA.LTTFNEIDMSNIQEMRARHKEAFLKKHNLKLG
Retrocopy LAEPGAGKGLHSEHREKKNRMWQCIAQRLKKAQNTCALLTTFNEIDMSNIQEMRARHKEAFLKKHNLKLG

Parental  FMSAFVKASAFALQEQPVVNAVIDDATKEVVYRDYIDISVAVATPRGLVVPVIRNVEAMNYADIERTITE
          FMSAFVKA.AFALQEQPVVNAVID..TKEV.YRDYIDISVAVATP.GLVVPVIRN.EAMNYADIE.TITE
Retrocopy FMSAFVKALAFALQEQPVVNAVIDNITKEVIYRDYIDISVAVATPQGLVVPVIRNLEAMNYADIEQTITE

Parental  LGEKARKNELAIEDMDGGTFTISNGGVFGSLFGTPIINPPQSAILGMHGIFDRPVAVGGKVEVRPMMYVA
          LGEKA.KNELAIEDMDGGTFTISNGGVFG.LFGTPIINPPQSAILGMHGIFDRPVA.GGKVEVRPMMYVA
Retrocopy LGEKA*KNELAIEDMDGGTFTISNGGVFGLLFGTPIINPPQSAILGMHGIFDRPVAIGGKVEVRPMMYVA

Parental  LTYDHRLIDGREAVTFLRKIKAAVEDPRVLLLDL
          LTYDHRL.DGREAVTFL.KIKAAVEDPRV.LLDL
Retrocopy LTYDHRLTDGREAVTFLGKIKAAVEDPRVVLLDL

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_1006 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009316	1 retrocopy	retro_cpor_1089,
Homo sapiens	ENSG00000119689	1 retrocopy	retro_hsap_407,
Gorilla gorilla	ENSGGOG00000011591	1 retrocopy	retro_ggor_403,
Nomascus leucogenys	ENSNLEG00000016330	1 retrocopy	retro_nleu_1006 ,
Oryctolagus cuniculus	ENSOCUG00000015606	1 retrocopy	retro_ocun_322,
Pan troglodytes	ENSPTRG00000006543	1 retrocopy	retro_ptro_312,
Tursiops truncatus	ENSTTRG00000001915	1 retrocopy	retro_ttru_681,
Xenopus tropicalis	ENSXETG00000013264	1 retrocopy	retro_xtro_46,