RetrogeneDB ID: retro_nleu_2148

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397332.1:4247178..4249131(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018441
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_2148
GAAGCACGAAGTTTGGAGGCAACCTGTGAAAAGCTGAACAGGTCCAATTCTGAACTTGAGGATGAAATCCTCTGTCTAGA
AAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTCAACAAGATGAATTGATGGCGGATATTTCAAAAAGGATACAGTCTC
TAGAAGATGAGTCAAAATCCCTCAAATCACAAATAGCTGAGGCCAAAATCATCTGCAAGTTATTTAAAATAACTGAAGAA
CGATGGGTGATAGCAATAAAAGATGCTTTGAATGAAAATTCTCAACATCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGC
TGAAGTATGGAAAGAACAAGACAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAGAACAAG
TTCTGAATGATAAAGAAAATCGCATCAAGACTCTGACTGGACACTTGCTAAAGATGAAAGATCAGGTTGCTGTGCTTGAA
GAAGACATAACAGATGATGATAACTTGGAATTAGAAGTGAACAGTCAATCGGAAAATGGTGCTTACTTAGATGATCCTCC
AAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAATTTAAATGTTTCTTTCAAAACCTTAGAAGGAGAAAGAAACCGCA
TTATTATTCAGTTATCGGAAGTTGATAAAACAAAGGAAGAGCTTACAGAGTATATGAAAAATCTTCAGACTCAACAAGCA
TCTTTGCAATCAGAAAACATATATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAATAATGACTGAATTATA
TCAAGAAAATGAAATGAAACTCCACAGGAAATTGACAATAGAGGAAAATTACCGGATAGAGGAAGAAGAGAAGCTTTCTA
AAGTGGAAGAAAAGATCAGCCGTGCCACTGAAGAGCTGGAGACCTATAGAAAGCTCGCCAAAGACCTTGAAGAAGAATTG
GAGAGAACTGTTCATTTTTATCAAAAGCAGGTTATTTCCTACGAGAAAAAAGGACATGATAATTGGTTGGCAGCTCGGAC
TGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAACTGAAACAGAGTTGAAATTTG
AACTTTTAGAAAAAGATCCTAATGCACTCGATGTTTCAAATACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCTGCA
CCATTGGGTCAGCCTTCATCTGAAACGAGAGCTTTTCCCTCTCCTCAAACTTTGTTGGAGAATCCACTCAGACTCTCACC
TGTGCTTCCAGCGGGAGGAGGAAGAGGCCCAAGCGGCCCAGGGAATCCCCTGGACCATCAGATTACCAATGGAAGAGGAG
AACCAAGCTGTGACAGGTTAATCGATCCTCACAGGGCTCCTTCTGACACTGGGTTCCTGAGATCTCCGTGGGAACAGGAC
CGCAGGATGTTGTTTCCTCCACCAGGGCAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTCATTC
TAATTCTGATAGACTGTCTGGACCAGCAGAACCCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGC
CTTCAGAAATGGAATCCAGTAGAAATGATGCCAAAGATGATCCTGGTAATTCAAATGTGCCTGATTCATCTCTCCCTGCT
GAAAATGAAGCATCTGGCCCCAGCTTTATTCCTCCACCTCTTGCTCCAATCAGCGGTCCATTGTTTCCAGTGGATACAAG
GGGCCCGTTCATGAGAAGAGGACCTCCTTTCCCCCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCGAGGTTATTTTC
CACTAAGGGATTTCCCAGGTCCACCACATGCTCCATTTGCAATGAGAAACATCTATCCACCGAGAGGTTTACCTCCTTAC
CTTCATCTGAGACCTGGATTTTACCCCAACCCC

Alignment

ORF - retro_nleu_2148 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.18 %
• Parental protein coverage: 80.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVKNQMATCEKLNRSNSELEDEILCLEKELKEEKCKHSEQDELMADISKRIQSLEDESKSLKSQVAEAKM
          E.....ATCEKLNRSNSELEDEILCLEKELKEEK.KHS.QDELMADISKRIQSLEDESKSLKSQ.AEAK.
Retrocopy EARSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSQQDELMADISKRIQSLEDESKSLKSQIAEAKI

Parental  TFKIFQMNEERLKIAIKDALTENSELQESQKQLLQDAEVWKEQVSELNKQKVTFEDSTVHAEQVLNDKEN
          ..K.F...EER..IAIKDAL.ENS..QESQKQLLQ.AEVWKEQ.SELNKQK.TFEDS.VHAEQVLNDKEN
Retrocopy ICKLFKITEERWVIAIKDALNENSQHQESQKQLLQEAEVWKEQDSELNKQKITFEDSKVHAEQVLNDKEN

Parental  HIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGE
          .IKTLT..LLKMKD..A.L.EDITDDDNLELE.NS.SENGAYLD.PPKGALKKLIHAA.LN.S.KTLEGE
Retrocopy RIKTLTGHLLKMKDQVAVLEEDITDDDNLELEVNSQSENGAYLDDPPKGALKKLIHAANLNVSFKTLEGE

Parental  RNQIYIQLSEVDTTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTV
          RN.I.IQLSEVD.TKEELTE..KNLQT.QASLQSEN..FE.ENQKLQQKLK.MTELYQENEMKLHRKLT.
Retrocopy RNRIIIQLSEVDKTKEELTEYMKNLQTQQASLQSENIYFESENQKLQQKLKIMTELYQENEMKLHRKLTI

Parental  EENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHENWLAARNAER
          EENYR.E.EEKLSKV.EKIS.ATEELETYRK.AKDLEEELERT.H.YQ.Q.IS.EKK.H.NWLAAR.AER
Retrocopy EENYRIEEEEKLSKVEEKISRATEELETYRKLAKDLEEELERTVHFYQKQVISYEKKGHDNWLAARTAER

Parental  NLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPASETRAFLSPPTLLE
          NLNDLRKENAHNRQKLTETELKFELLEKDP.ALDV.NTAFGREHSPYGP.PLG.P.SETRAF.SP.TLLE
Retrocopy NLNDLRKENAHNRQKLTETELKFELLEKDPNALDVSNTAFGREHSPYGPAPLGQPSSETRAFPSPQTLLE

Parental  GPLRLSPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWEQDRRMMFPPPGQ
          .PLRLSP.LP.GGGRG..GPGNP.DHQITN.RGE.SCDRL.DPHRAPSDTG.L..PWEQDRRM.FPPPGQ
Retrocopy NPLRLSPVLPAGGGRGPSGPGNPLDHQITNGRGEPSCDRLIDPHRAPSDTGFLRSPWEQDRRMLFPPPGQ

Parental  SYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSKDDLGNLNVPDSSLPA
          SYPDSALPPQR.DRF.SNS.RLSGPAE.RSFNMPSLDKMDGSMPSEME.SRND.KDD.GN.NVPDSSLPA
Retrocopy SYPDSALPPQREDRFHSNSDRLSGPAEPRSFNMPSLDKMDGSMPSEMESSRNDAKDDPGNSNVPDSSLPA

Parental  ENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPHAPFAMRN
          ENEA.GP.F.PPPLAPI.GPLFPVDTRGPF.RRGPPFPPPPPG.MFGASR.YFP.RDFPGPPHAPFAMRN
Retrocopy ENEASGPSFIPPPLAPISGPLFPVDTRGPFMRRGPPFPPPPPGTMFGASRGYFPLRDFPGPPHAPFAMRN

Parental  VYPPRGFPPYLPPRPGFFPPP
          .YPPRG.PPYL..RPGF.P.P
Retrocopy IYPPRGLPPYLHLRPGFYPNP

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_2148 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.

---

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,