RetrogeneDB ID: retro_nleu_3077

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397835.1:33088..35104(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018643
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_nleu_3077
GAGTTTGAAGGCTATGAAGTAGAGTCATCTTTAGAGAATGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTTGGA
GGCAACCTGTGAAAAGTTGAACAGGTCCAACTCTGAACTTGAGGATGAAATCCTCTGTCTAGAAAAAGAGTTAAAAGAAG
AGAAATCTAAACATTCTCAACAAGATGAATTGATGGCGGATATTTCAAAAAGGATACAGTCTCTAGAAGATGAGTCAAAA
TCCCTCAAATCACAAATAGCTGAAGCCAAAATCATCTGCAAGATATTTAAAATAACTGAAGAACGATGGGCGATAGCAAT
AAAAGATGCTTTGAATGAAAATTCTCAACTTCAGAAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAGAAC
AAGACAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAGAACAAGTTCTGAATGATAAAGAA
AATCGCATCAAGACTCTGACTGGACACTTGCTAAAGATGAAAGATCAGGTTGCTGTGCTTGAAGAAGACACAACGGATGA
TGATAACTTGGAATTAGAAGTGAACAGTCAATCGGAAAATGGTGCTTACTTAGATGATCCTCCAAAAGGAGCTTTGAAGA
AACTGATTCATGCTGCTAAGTTAAATGTTTCTTTCAAAACCTTAGAAGGAGAAAGAAACCGCATTATTATTCAGTTATCT
GAAGTGGACAAAACAAAGGAAGAGCTTACAGAGTATATGAAAAATATTCAGACTCAACAAGCATCTTTGCAGTCAGAAAA
CATATATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAATAATGACTGAATTATATCAAGAAAATGAAATGA
AACTCCACAGGAAATTGACAATAGAGGAAAATTACCGGATAGAGGAAGAAGAGAAACTTTCTAAAGTGGAAAAAAAGATC
AGCCGTGCCACTGAAGAGCTGGAGACCTATAGAAAGCTCGCCAAAGACCTTGAAGAAGAATTGGAGAGAACTGTTCATTT
TTATCAAAAGCAGGTTATTTCCTACGAGAAAAAAGGACATGATAATTGGTTGGCAGCTCGGACTGCTGAAAGAAACTCCA
ATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAACTGAAACAGAGTTGAAATTTGAACTTTTAGAAAAAGAT
CCTAATGCACTCGATGTTTCAAATACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCACACCATTGGGTCAGCCTTC
ATCTGAAACGAGAGCTTGTCCCTCCCTTCAAACTTTGTTGGAGGATACACTCAGACTCTCACCTGTGCATCCAAGAGGAG
GAGGAAGAGGCCCAAGAGGCCCAGGGAATCCCCTGGACCATCAGATTACCAATGAAAGAGGAGAACCAAGCTGTGATAGG
TTAACTGATCCTCACAGGGCTCCTTCTGACACTGGGTTCCTGCCATCTCCGCGGGAACAGGACCGTAAGATGATGTTTCC
TCCACCAGGGCAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTTATTCTAATTCTGATAGACTGT
CTGGACCAGCAGAACCCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGTCTTCAGAAATGGAATCC
AGTAGAAATGATGCCAAAGATGATCCTGGTAATTCAAATGTGCCTGATTCATCTCTCCCTGCTGAAAATGAAGCATCTGG
CCCCAGCTTTATTCCTCCACCTCTTGCTCCAATCAGCGGTCCATTGTTTCCAGTGGATACAAGGGGCCCATTCATGAGAA
GAGGACCTCCTTTCCCCCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCAAGGTTATTTTCCACCAAGGGATTTCCCA
GGTCCACCACATGCTCCATTTGCAATGAGAAACATCTATCCACCGAGGGGTTTACCTCCCTACCTTCATCTGAGACCTGG
ATTTTACCCCAACCCC

Alignment

ORF - retro_nleu_3077 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 83.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVESSLKDASFEKEATEAQSLEVKNQMATCEKLNRSNSELEDEILCLEKELKEEKCKHSEQDELMADISK
          E.E......S.E....E....E.....ATCEKLNRSNSELEDEILCLEKELKEEK.KHS.QDELMADISK
Retrocopy EFEGYEVESSLENASFEKAAAEARSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSQQDELMADISK

Parental  RIQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALTENSELQESQKQLLQDAEVWKEQVSELNK
          RIQSLEDESKSLKSQ.AEAK...KIF...EER..IAIKDAL.ENS.LQ.SQKQLLQ.AEVWKEQ.SELNK
Retrocopy RIQSLEDESKSLKSQIAEAKIICKIFKITEERWAIAIKDALNENSQLQKSQKQLLQEAEVWKEQDSELNK

Parental  QKVTFEDSTVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKG
          QK.TFEDS.VHAEQVLNDKEN.IKTLT..LLKMKD..A.L.ED.TDDDNLELE.NS.SENGAYLD.PPKG
Retrocopy QKITFEDSKVHAEQVLNDKENRIKTLTGHLLKMKDQVAVLEEDTTDDDNLELEVNSQSENGAYLDDPPKG

Parental  ALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDTTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQK
          ALKKLIHAAKLN.S.KTLEGERN.I.IQLSEVD.TKEELTE..KN.QT.QASLQSEN..FE.ENQKLQQK
Retrocopy ALKKLIHAAKLNVSFKTLEGERNRIIIQLSEVDKTKEELTEYMKNIQTQQASLQSENIYFESENQKLQQK

Parental  LKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQG
          LK.MTELYQENEMKLHRKLT.EENYR.E.EEKLSKV..KIS.ATEELETYRK.AKDLEEELERT.H.YQ.
Retrocopy LKIMTELYQENEMKLHRKLTIEENYRIEEEEKLSKVEKKISRATEELETYRKLAKDLEEELERTVHFYQK

Parental  QIISHEKKAHENWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGP
          Q.IS.EKK.H.NWLAAR.AERN.NDLRKENAHNRQKLTETELKFELLEKDP.ALDV.NTAFGREHSPYGP
Retrocopy QVISYEKKGHDNWLAARTAERNSNDLRKENAHNRQKLTETELKFELLEKDPNALDVSNTAFGREHSPYGP

Parental  SPLGWPASETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPSD
          .PLG.P.SETRA..S..TLLE..LRLSP..P.GGGRG.RGPGNP.DHQITNERGE.SCDRLTDPHRAPSD
Retrocopy TPLGQPSSETRACPSLQTLLEDTLRLSPVHPRGGGRGPRGPGNPLDHQITNERGEPSCDRLTDPHRAPSD

Parental  TGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEP
          TG.L..P.EQDR.MMFPPPGQSYPDSALPPQR.DRF.SNS.RLSGPAE.RSFNMPSLDKMDGSM.SEME.
Retrocopy TGFLPSPREQDRKMMFPPPGQSYPDSALPPQREDRFYSNSDRLSGPAEPRSFNMPSLDKMDGSMSSEMES

Parental  SRNDSKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFGAS
          SRND.KDD.GN.NVPDSSLPAENEA.GP.F.PPPLAPI.GPLFPVDTRGPF.RRGPPFPPPPPG.MFGAS
Retrocopy SRNDAKDDPGNSNVPDSSLPAENEASGPSFIPPPLAPISGPLFPVDTRGPFMRRGPPFPPPPPGTMFGAS

Parental  RDYFPPRDFPGPPHAPFAMRNVYPPRGFPPYLPPRPGFFPPP
          ..YFPPRDFPGPPHAPFAMRN.YPPRG.PPYL..RPGF.P.P
Retrocopy QGYFPPRDFPGPPHAPFAMRNIYPPRGLPPYLHLRPGFYPNP

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_3077 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,