RetrogeneDB ID: retro_nleu_3017

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397579.1:360181..362206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_nleu_3017
GCAACCTGTGAAAAGCTAAACAGGTCCAGTTCTGAACTTGAGAATGAAATACTCTGTCTAGAAAAAGAGTTAAAATAAGA
GAAATCTAAACATTCTGAACAAGGTGAATTGATGGTGGATATTTGCAAAATGATACAGTCTCTAAAAGATGAGTCAAAAT
CCCTCAAATCACAAGTAGCTGAAGCCAAAATGAACTTCACGATATTTCAAATGAATGAAGAACGACTGAAGATAGCAATA
AAAGATGCTTTGAATGAACATTCTAAACTTCAGGAAAACGAGAAACAGCTTTTTCAAGAAGCTGAGGTATGGAAAGAACA
CGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAGAACAAGTTCTAAATGATAAAGAAA
ATCACATCAAGACTCTGACTGAATGCTTGCTAAAAATGAAAGATCAGGCTGCTATGCTTGGAGAAGACATAACGGATGAT
GGTAACTTGGAATTAGAAACGAACAGTGAATCGGAAAATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAA
ACTGATTTATGCTGCTAAGTTAAATGCTTCTTTAAAAATCTTAGAAGGAGAAAGAAACCAAATTTATAGTCAGTTATCTG
AAGTTGATAAAACAAAGGAAGAGCTTGCAGAGCATATTAAAAATCTTCAGACTGAACAAGCATCTTTGCAGTCAGAAAAC
ACAAATTTGAAAGTGAGAATCAGAAGCTTCAACAAAAACTTAAAGTGAAGATTGAATTATATCAAGAAAATGAAATGAAA
CTCCAGAGGAAATTAACAGTAGAGGAAAATTACCGGTTAGAGAAGGAAGAGAAACTTTCTAAAGTACACGAAAAGATTAG
CCATGCCACTGAAGAGTTGGAGACCTATAGAAAGTGAGCTAAAGATCTTGAAGAAGAGTTGGAGAGAACTATTCATTCTT
ATCAAGGATGGATTATTTCCCACGAGAAAAGAGCACATAATAATTGGTTGGCAGCTTGGACTGCTGAAAGAAACCTCAAT
GATTTAAGGAAAGAAAGTGCTCACAACAGACAAAAATTAACTGAAGCACAGTTTAAATTTGAACTTTTAGAAAAAGATCC
TTATGCACTTTATGTTCCAAATACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGCCGGCCTTCAT
CTGAAACAAGAGTTTTTCTCTGTCCTCCAACTTTGTTGGCGGGCCCACTCAGACTCTCATCTTTGCTAACAGGAGGAGGA
GGAAGAGGCTCAACAGGTCCAGGGAATCCTCTGGACCATCAGATTACCAATGAAAGAGGAGAATCAAGATGTGATAGGTT
AACCAATCCTCACAGGGCTTCTTCTGACACTGGGTCCCTGTCACCTCCATGGGAACAGGACTGTAGGATGATGTTTCCTC
CACCAGGACAGTCATGTCTTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAATTCTGGCACACTGTCT
GGACCAGCAGAACTCAGAAGGTTTAATATGACTTCTTTGGATAAAATGGATGGGTCAATGCTTTCAGAAATGGAATCCAG
TAGAAATGATGCCAAAGATGACTTTGGTAATTTAAATGTGCCTGATTCATCTCTCCCCACTGAAAATGAAGCAACTGGCC
CTCACTTTTTTCCTCCACCTGTTGGTCCAATCAGAGGTCCATTGTTTCTGGGGGATACAAGTGCCAGTTCATGAGAAGAG
GACCTCCTTTCCCCCCATCTTCTCCAGGAACTGTGTTTGGAGCTTCTCAAGATTATTTTCCACCAAGGGATTTCCCAGAT
CCACCACATGCTCCATTTGCATGAGAAATGTTTATCCACCGAGGGGTTTCCTCCTTACCTTCCCCTGAGACCTGGATTTT
TCCCCCTAAACCCCACATTCTGAAGGTAGAAGTGAGTTCCCTGCAGGGTTGATTCTGCCTTCAAATGAGCCCACTATTGA
ACATCCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_nleu_3017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.32 %
• Parental protein coverage: 83.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  ATCEKLNRSNSELEDEILCLEKELKEEKCKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKMTFKIFQ
          ATCEKLNRS.SELE.EILCLEKELK.EK.KHSEQ.ELM.DI.K.IQSL.DESKSLKSQVAEAKM.F.IFQ
Retrocopy ATCEKLNRSSSELENEILCLEKELK*EKSKHSEQGELMVDICKMIQSLKDESKSLKSQVAEAKMNFTIFQ

Parental  MNEERLKIAIKDALTENSELQESQKQLLQDAEVWKEQVSELNKQKVTFEDSTVHAEQVLNDKENHIKTLT
          MNEERLKIAIKDAL.E.S.LQE..KQL.Q.AEVWKE.VSELNKQK.TFEDS.VHAEQVLNDKENHIKTLT
Retrocopy MNEERLKIAIKDALNEHSKLQENEKQLFQEAEVWKEHVSELNKQKITFEDSKVHAEQVLNDKENHIKTLT

Parental  ERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYI
          E.LLKMKD.AAMLGEDITDD.NLELE.NSESENGAYLDNPPKGALKKLI.AAKLNASLK.LEGERNQIY.
Retrocopy ECLLKMKDQAAMLGEDITDDGNLELETNSESENGAYLDNPPKGALKKLIYAAKLNASLKILEGERNQIYS

Parental  QLSEVDTTKEELTEHIKNLQTEQASLQSENTH-FENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYR
          QLSEVD.TKEEL.EHIKNLQTEQASLQSENT..FE.ENQKLQQKLKV..ELYQENEMKL.RKLTVEENYR
Retrocopy QLSEVDKTKEELAEHIKNLQTEQASLQSENTN<FESENQKLQQKLKVKIELYQENEMKLQRKLTVEENYR

Parental  LEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHENWLAARNAERNLNDL
          LEKEEKLSKV.EKISHATEELETYRK.AKDLEEELERTIHSYQG.IISHEK.AH.NWLAA..AERNLNDL
Retrocopy LEKEEKLSKVHEKISHATEELETYRK*AKDLEEELERTIHSYQGWIISHEKRAHNNWLAAWTAERNLNDL

Parental  RKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPASETRAFLSPPTLLEGPLRL
          RKE.AHNRQKLTE...KFELLEKDPYAL.VPNTAFGREHSPYGPSPLG.P.SETR.FL.PPTLL.GPLRL
Retrocopy RKESAHNRQKLTEAQFKFELLEKDPYALYVPNTAFGREHSPYGPSPLGRPSSETRVFLCPPTLLAGPLRL

Parental  SPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDS
          S.LL.GGGGRGS.GPGNP.DHQITNERGES.CDRLT.PHRA.SDTGSLSPPWEQD.RMMFPPPGQS..DS
Retrocopy SSLLTGGGGRGSTGPGNPLDHQITNERGESRCDRLTNPHRASSDTGSLSPPWEQDCRMMFPPPGQSCLDS

Parental  ALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSKDDLGNLNVPDSSLPAENEAT
          ALPPQRQDRF.SNSG.LSGPAELR.FNM.SLDKMDGSM.SEME.SRND.KDD.GNLNVPDSSLP.ENEAT
Retrocopy ALPPQRQDRFYSNSGTLSGPAELRRFNMTSLDKMDGSMLSEMESSRNDAKDDFGNLNVPDSSLPTENEAT

Parental  GPGFVPPPLAPIRGPLFPVDT-RGPFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPHAPFA-MRNVYP
          GP.F.PPP..PIRGPLF..DT....F.RRGPPFPP..PG..FGAS.DYFPPRDFP.PPHAPFA.MRNVYP
Retrocopy GPHFFPPPVGPIRGPLFLGDT<KCQFMRRGPPFPPSSPGTVFGASQDYFPPRDFPDPPHAPFA<MRNVYP

Parental  PR-GFPPYLPPRPGFFPP-PPHSEGRSEFPSGLIPPSNEPATEHPERQQET
          PR.GFPPYLP.RPGFFP...PHSEGRSEFP.GLI.PSNEP..EHPE.QQET
Retrocopy PR<GFPPYLPLRPGFFPL>TPHSEGRSEFPAGLILPSNEPTIEHPEPQQET

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_3017 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,