RetrogeneDB ID: retro_nleu_2422

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397353.1:6585639..6586487(-)
• Located in intron of: ENSNLEG00000014271

Retrocopy information

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

Parental gene information

• Parental gene symbol: PEF1
• Ensembl ID: ENSNLEG00000001979
• Aliases: None
• Description: None

Sequence

>retro_nleu_2422
ATGGCCAGCTATCTGTATGGGCAGGGCTGCCCCGGAGATGCAGGACAAGCGCCAGGAACCCCTCCGGGTAGCTACTATCC
TGGACCCCCAATAGTGGAGGGCAGTATAGCAGCGTGCTACCCCCTGGTGGTGGTTATGGGGCTCCTGCCCCTGGAGGGCC
TTATGGACCACCAGCTGGTAGAGGGCCCTATGGACACCTCAATCCTGGGATGTTCCCCTCTGGAACTCCAGGAGGACAAA
ATGACGGTGCAGCTCCAGGGGGCCCCTATGGTCAGCCACCTCCAAATTCCTATGGTGCCCAGCAGACCAGGCTTTATGGA
CAGGGTGGCTCTCCTCCCAATATGGATGAAGCCTACTCCTGGTTCCAGTCGGTGACTCTGATTACAGTGGTTTTATCTCC
ATGAAGGAGGTGAAGCAGGCTCTGGTCAACTGCAACTGGTCCTTGTTCAATGATGGGACCTGCCTCATGATGATAAACAT
GTTTGACAAGACCTAATCAGGCCACATCAATGTCTATGGCTTCTCAGCCCTGTGGAAATTCATCCAGCAGTGGAAGCAGC
TCTTCCAGCAGTTATGACCGGGAAAACTCAGGCTCCATTAGCTACACAGAGCTGCAGCAAGCTCTGTCCCAAATGGGCTA
CCACCTGAGCCCCCAGTTCACCCAGCTACTGGTCTCTAGCTACTGCCCACACTCTGCCAATCCTGCCAGGCAGCTTGATC
GCTTCATCCAGGTGTGCACCCAGCTGCAGGTGCCGACAGAGGCCTTCTGGGAGAAGGACACAGCTGTACAAGGCAACATT
CGGCTCAGCTTCAAGGACGTCGTTACCATGACAGCTTTTCGGATGCTA

Alignment

ORF - retro_nleu_2422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MASYPYRQGCPGAAGQAPGAPPGSYYPGPP-NSGGQYGSGLPPGGGYGGPAPGGPYGPPAGGGPYGHPNP
          MASY.Y.QGCPG.AGQAPG.PPGSYYPGPP.NSGGQY.S.LPPGGGYG.PAPGGPYGPPAG.GPYGH.NP
Retrocopy MASYLYGQGCPGDAGQAPGTPPGSYYPGPP<NSGGQYSSVLPPGGGYGAPAPGGPYGPPAGRGPYGHLNP

Parental  GMFPSGTPGGPYGGAAPGGPYGQPPPSSYGAQQPGLYGQGGAPPNVDPEAYSWFQSV-DSDHSGYISMKE
          GMFPSGTPGG...GAAPGGPYGQPPP.SYGAQQ..LYGQGG.PPN.D.EAYSWFQSV.DSD.SG.ISMKE
Retrocopy GMFPSGTPGGQNDGAAPGGPYGQPPPNSYGAQQTRLYGQGGSPPNMD-EAYSWFQSV<DSDYSGFISMKE

Parental  LKQALVNCNWSSFNDETCLMMINMFDKTKSGRIDVYGFSALWKFIQQWKNLFQQ-YDRDRSGSISYTELQ
          .KQALVNCNWS.FND.TCLMMINMFDKT.SG.I.VYGFSALWKFIQQWK.LFQQ.YDR..SGSISYTELQ
Retrocopy VKQALVNCNWSLFNDGTCLMMINMFDKT*SGHINVYGFSALWKFIQQWKQLFQQ>YDRENSGSISYTELQ

Parental  QALSQMGYNLSPQFTQLLVSRYCPRSANPAMQLDRFIQVCTQLQVLTEAFREKDTAVQGNIRLSFEDFVT
          QALSQMGY.LSPQFTQLLVS.YCP.SANPA.QLDRFIQVCTQLQV.TEAF.EKDTAVQGNIRLSF.D.VT
Retrocopy QALSQMGYHLSPQFTQLLVSSYCPHSANPARQLDRFIQVCTQLQVPTEAFWEKDTAVQGNIRLSFKDVVT

Parental  MTASRML
          MTA.RML
Retrocopy MTAFRML

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_2422 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006355	1 retrocopy	retro_cjac_1745,
Homo sapiens	ENSG00000162517	1 retrocopy	retro_hsap_497,
Gorilla gorilla	ENSGGOG00000015897	1 retrocopy	retro_ggor_464,
Macropus eugenii	ENSMEUG00000014458	1 retrocopy	retro_meug_375,
Microcebus murinus	ENSMICG00000001374	1 retrocopy	retro_mmur_937,
Macaca mulatta	ENSMMUG00000023397	1 retrocopy	retro_mmul_146,
Monodelphis domestica	ENSMODG00000017573	1 retrocopy	retro_mdom_1930,
Nomascus leucogenys	ENSNLEG00000001979	1 retrocopy	retro_nleu_2422 ,
Oryctolagus cuniculus	ENSOCUG00000005744	1 retrocopy	retro_ocun_461,
Pongo abelii	ENSPPYG00000001611	1 retrocopy	retro_pabe_238,
Pan troglodytes	ENSPTRG00000000463	1 retrocopy	retro_ptro_375,
Rattus norvegicus	ENSRNOG00000013972	2 retrocopies	retro_rnor_1563, retro_rnor_2505,