RetrogeneDB ID: retro_nleu_1218

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397285.1:15171518..15173598(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000006805
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000004121
• Aliases: None
• Description: None

Sequence

>retro_nleu_1218
GAGCCATCTTTAAAGGATGCCAGCTTTGAGAAGGAGGCAACAGAAGTACAAAGTTTGGAGGCAACCTGCGAAAAGCTGAA
CAGGTTCAATTCTGAACTTGAGCATGAAATACTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTGAAC
AAAATCAATTGATGGCAGATATTTGCAAAAGGATACGGTCGCTAGAAGATGAGTCAAAATCCCTCAAATCACAAGTAGCT
GAAGCCAAAATGACCTTCAAGAGATTTCAAATGAATGAAGAACAACTGGAGATAGAAATACGAGATGCTTTGAATGAAAA
TTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAGGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTATTAGAC
AGAAAAGAACATTTGAAGACTCCAAAGTACACGTAGAACAAGTTCTAAATGATAAAGAAAATCACATCAAGACTGACTGA
ACGCTTGCTAAAGATGAAAGATGGCGTTGCTATGCTTGAAGAAGACGTAATGTATGATGATAACTTGGAATTAGAAATGA
ACAGTGAATCGGAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCACACTGCTAAGTTA
AATGCTTCTTTAAAAACCTTAGGAGAAAGAAACCAAATTTATATTCAATTATCTGAAGTTGATAAAACAAAGGAAGAGCT
TACAGAGCATATTAAAAATCTTCAGACTGAACAAGCATCTATGCAGTCAGAAAACACACATTTTGGAAGTGAGAATCAGA
AGCTTCAGCAGAAACTTAAAGTAATGACTGAATTATATCAAGAACGTGAAATGAAACTCTACAGGAAATTAATAGTAGAG
GAAAAATACCATTTAGAGAAAGAAGAGAAACTTTCTAAAGTAGACGAAATGATCAGCCATGCCACTGAAGAGCTGGAGAC
CTACCGAAAGCGAGCCAAAGATCTTAAAGAATTTGAGAGAACTATTCATTTTTATCAAAAGAAGATTATTCTCCATGAGA
AAAAAGCACACGATAATTGGTCGGCAGCTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAAC
AGACAAAAATTAACTGAAATAGAGTTTAAAATAAAACTTTTAGAAAAAGATCCTTATGGACTTGATGTTCCAAATACAGC
ATTTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTCTCTCTATCCTC
CAACTTTATTGGAGGGTCCTCCCAGACTCTCACCTTTGCTTCCAGAGGGAGGAGGAAGAGGCTCCAGAGGCCCAGGGAAT
CCTCTGGACCATCAGATTACCAATGAAAGAGGAGAATCAAGCTGTGATAGGTTAACTGATCCTCACAGGGCTCCTTCTGA
CACTGGGCCCCTGTCACCTTCGTGGGAACAGGACTGTAGGATGGTATTTCCTCCACCAGGACAATCATATCCTGATTCAG
CTCTTCCTCCACAAAGGCAAGATAGATTTCATTCTAATTGTGCTAGACTCTCTGGACCAGCAGAACTCAGAAGTTTTAAT
ATGCCTTCTTTGGCTAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAACGATACCAAAGATAATCTTGG
TGATTTAAAGGTGCCTGATTCATCTCTCCCCACTGAAAATGAAGCAACTGGCCCTGGCTTTGTTCCTCTACCTCTTGCTC
CAATCAGAGGTTCATTGCTTCCAGTAGATACAAGGGGCCCGTTCATGAGAAGAGGACCTCCTTTCCCCCCACCTCCTCCA
GGAACCGTGTTTGGAGCTTCTCCAGGTTATTTTCCACCAAGGGATGTCCCAGGTCCACCACGTGCTCCATTTGCAATGAG
AAATGTCTATCTACCGAGAGGTTTTCCTCCTTACTGTCCCCCAAGACCTGGATTTTTCCCCCCAACCCCCACATTTTGAA
GGTAGAATGAGTTTCCATCAGGGTTGAGTCCAACTTCAATTGAGCCTGCTGCTGAATATCCAGAAAGACAGCAAGAAACC

Alignment

ORF - retro_nleu_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.69 %
• Parental protein coverage: 86.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DASFEKEATEAQSLEVKNQMATCEKLNRSNSELEDEILCLEKELKEEKCKHSEQDELMADISKRIQSLED
          ..S......E....EV....ATCEKLNR.NSELE.EILCLEKELKEEK.KHSEQ..LMADI.KRI.SLED
Retrocopy EPSLKDASFEKEATEVQSLEATCEKLNRFNSELEHEILCLEKELKEEKSKHSEQNQLMADICKRIRSLED

Parental  ESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALTENSELQESQKQLLQDAEVWKEQVSELNKQKVTFED
          ESKSLKSQVAEAKMTFK.FQMNEE.L.I.I.DAL.ENS.LQESQKQLLQ.AEVWKEQVSEL..QK.TFED
Retrocopy ESKSLKSQVAEAKMTFKRFQMNEEQLEIEIRDALNENSQLQESQKQLLQEAEVWKEQVSELIRQKRTFED

Parental  STVHAEQVLNDKENHIKTLTERLLKMKDW-AAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLI
          S.VH.EQVLNDKENHIKT....L.K...W..AML.ED...DDNLELEMNSESE.GAYLDNPPKGALKKLI
Retrocopy SKVHVEQVLNDKENHIKT-D*TLAKDERW>VAMLEEDVMYDDNLELEMNSESEDGAYLDNPPKGALKKLI

Parental  HAAKLNASLKTLEGERNQIYIQLSEVDTTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTE
          H.AKLNASLKTL.GERNQIYIQLSEVD.TKEELTEHIKNLQTEQAS.QSENTHF..ENQKLQQKLKVMTE
Retrocopy HTAKLNASLKTL-GERNQIYIQLSEVDKTKEELTEHIKNLQTEQASMQSENTHFGSENQKLQQKLKVMTE

Parental  LYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHE
          LYQE.EMKL.RKL.VEE.Y.LEKEEKLSKVDE.ISHATEELETYRKRAKDL..E.ERTIH.YQ..II.HE
Retrocopy LYQEREMKLYRKLIVEEKYHLEKEEKLSKVDEMISHATEELETYRKRAKDL-KEFERTIHFYQKKIILHE

Parental  KKAHENWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWP
          KKAH.NW.AA..AERNLNDLRKENAHNRQKLTE.E.K..LLEKDPY.LDVPNTAFGREHSPYGPSPLG.P
Retrocopy KKAHDNWSAAWTAERNLNDLRKENAHNRQKLTEIEFKIKLLEKDPYGLDVPNTAFGREHSPYGPSPLGRP

Parental  ASETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPSDTGSLSP
          .SETRA.L.PPTLLEGP.RLSPLLP.GGGRGSRGPGNP.DHQITNERGESSCDRLTDPHRAPSDTG.LSP
Retrocopy SSETRASLYPPTLLEGPPRLSPLLPEGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGPLSP

Parental  PWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSK
          .WEQD.RM.FPPPGQSYPDSALPPQRQDRF.SN..RLSGPAELRSFNMPSL.KMDGSMPSEME.SRND.K
Retrocopy SWEQDCRMVFPPPGQSYPDSALPPQRQDRFHSNCARLSGPAELRSFNMPSLAKMDGSMPSEMESSRNDTK

Parental  DDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFGASRDYFPP
          D.LG.L.VPDSSLP.ENEATGPGFVP.PLAPIRG.L.PVDTRGPF.RRGPPFPPPPPG..FGAS..YFPP
Retrocopy DNLGDLKVPDSSLPTENEATGPGFVPLPLAPIRGSLLPVDTRGPFMRRGPPFPPPPPGTVFGASPGYFPP

Parental  RDFPGPPHAPFAMRNVYPPRGFPPYLPPRPGFFPP-PPHSEGR-SEFPSGLIPPSNEPATEHPERQQET
          RD.PGPP.APFAMRNVY.PRGFPPY.PPRPGFFPP.PPH.EGR..EFPSGL.P.S.EPA.E.PERQQET
Retrocopy RDVPGPPRAPFAMRNVYLPRGFPPYCPPRPGFFPP>PPHFEGR<NEFPSGLSPTSIEPAAEYPERQQET

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_1218 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 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218 , retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503, retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,