RetrogeneDB ID: retro_nleu_1690

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397304.1:13001070..13002690(-)
• 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_1690
AATCACATCAAGACTCTGACTGGACACTTGCTAAAGATGAAAGATTAGGCTGCTATGCTTGAAGAAGACACAACGGACGA
TGATAACTTGGAATTAGAAGTGAACAGTCAATGGAAAATGGTGCTTACTTAGATGATCCTCCAAAAGGAGCTTTGAAGAA
ACTGATTCATGCTGCTAAGTTAAATGTTTCTTTAAAAACCTCAGAAGGAGAAAGAAACCACATTATTATTCAGTTATCTG
AAGTGGGCAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTCAACAAGCATCTTTGCAGTCAGAAAAC
ATGTATTTTGAAAGTGAGAATCAGAAGCTGCAACTTGAAATGATGACTGAATTATATCAAGAAGATGAAATGACACTCCA
CAGGAAACTGACAATAGAGGAAAATTACCGGATAGAGGAAGAAGAGAAGCTTTCTAAAGTGGAAGAAAAGATCAGCCATG
CCACTGAAGAGCTGGAGACCTATAGAAAGCTAGCCAAAGATCTTGAAGAAGAATTGGAGAGAACTGTTCATTTTTATCAA
AAGCAGGTTATTTCCTACGAGAAAAAAGGACATGATAATTGGTTGGCAGCTCGGACTGCTGAAAGAAACCTCAATGATTT
AAGGAAAGAAAATGCTCACAACAAACAAAAATTAACTGAAACAGAGTTCAAATTTGAACTTTCAGAAAAAGATACTAATG
CACTTGATGTTTCAAATACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCCTCACCATTGGGTCAGCCTTCATCTGAA
ACGAGAGCTTTTCTCTCTCCTCAAACTTTGTTGGAGGATCCACTCAGACTCTCACCTGTGCTTCCAGGGAGAGGAGGAAG
AAGCCCAAGCGGCCCAGGGAATCCTCTGGACCATCAGATTACCAATAAAAGAGGAGAACCAAGCTGTGACAGGTCAACTG
ATGCTCACAGGGCTCCTTCTGACACTGGGTCCCTGTCATCTCCACGGGAACAGGATCGTAGGATGATGGTTCCTCCACCA
AGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGGAAGACAGATTTTATTCTAATTCTGATAGACTGTCTGGACC
AGCAGAACTCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGCCCTCAGAAATGGAATCCACTAGAA
ATGATGCCAAAGATGATCCTGGTAGTTTAAATGTGCCTGATTCATCTCTCCCTGCTGAAAATGAAGCAACTGGCCCCGGC
TTTATTCCTCCACCTCTTGCTCCAATCAGCGGTCCACTGTTTCCAGGGGATACAAGGGGTCCATTCATGAGAAGAGGACC
TCCTTTCCCCCCACCTCCTCCAGGAACCATGTTTGGAGCTTCACGAGGTTATTTTCTACCAAGGGATTTCCCAGGTCCAC
CACATGCTCCATTTGCAATGAGAAACATCTATCCACCGAGGGGTTTACCTCCTTACTTTCATCCAAGACCTGGATTTTAC
CCCAACCCCACATTCCGAAGGTAGAAGCGAGTTCCCTTCAGGGTTGCTTCCGCCTTCAAAGGAGCCTGCTACTGAACATC
CAGAACCACAGCAAGAAACC

Alignment

ORF - retro_nleu_1690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.6 %
• Parental protein coverage: 67.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSE-SENGAYLDNPPKGALKKLIHAAKLNASLKTLE
          NHIKTLT..LLKMKD.AAML.ED.TDDDNLELE.NS...ENGAYLD.PPKGALKKLIHAAKLN.SLKT.E
Retrocopy NHIKTLTGHLLKMKD*AAMLEEDTTDDDNLELEVNSQ<MENGAYLDDPPKGALKKLIHAAKLNVSLKTSE

Parental  GERNQIYIQLSEVDTTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKL
          GERN.I.IQLSEV..TKEELTEHIKNLQT.QASLQSEN..FE.ENQKLQ..L..MTELYQE.EM.LHRKL
Retrocopy GERNHIIIQLSEVGKTKEELTEHIKNLQTQQASLQSENMYFESENQKLQ--LEMMTELYQEDEMTLHRKL

Parental  TVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHENWLAARNA
          T.EENYR.E.EEKLSKV.EKISHATEELETYRK.AKDLEEELERT.H.YQ.Q.IS.EKK.H.NWLAAR.A
Retrocopy TIEENYRIEEEEKLSKVEEKISHATEELETYRKLAKDLEEELERTVHFYQKQVISYEKKGHDNWLAARTA

Parental  ERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPASETRAFLSPPTL
          ERNLNDLRKENAHN.QKLTETE.KFEL.EKD..ALDV.NTAFGREHSPYGPSPLG.P.SETRAFLSP.TL
Retrocopy ERNLNDLRKENAHNKQKLTETEFKFELSEKDTNALDVSNTAFGREHSPYGPSPLGQPSSETRAFLSPQTL

Parental  LEGPLRLSPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWEQDRRMMFPPP
          LE.PLRLSP.LPG.GGR...GPGNP.DHQITN.RGE.SCDR.TD.HRAPSDTGSLS.P.EQDRRMM.PPP
Retrocopy LEDPLRLSPVLPGRGGRSPSGPGNPLDHQITNKRGEPSCDRSTDAHRAPSDTGSLSSPREQDRRMMVPPP

Parental  GQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSKDDLGNLNVPDSSL
          .QSYPDSALPPQR.DRF.SNS.RLSGPAELRSFNMPSLDKMDGSMPSEME..RND.KDD.G.LNVPDSSL
Retrocopy RQSYPDSALPPQREDRFYSNSDRLSGPAELRSFNMPSLDKMDGSMPSEMESTRNDAKDDPGSLNVPDSSL

Parental  PAENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPHAPFAM
          PAENEATGPGF.PPPLAPI.GPLFP.DTRGPF.RRGPPFPPPPPG.MFGASR.YF.PRDFPGPPHAPFAM
Retrocopy PAENEATGPGFIPPPLAPISGPLFPGDTRGPFMRRGPPFPPPPPGTMFGASRGYFLPRDFPGPPHAPFAM

Parental  RNVYPPR-GFPPYLPPRPGFFPPP-PHSEGRSEFPSGLIPPSNEPATEHPERQQET
          RN.YPPR.GF...L.......P.P.PHSEGRSEFPSGL.PPS.EPATEHPE.QQET
Retrocopy RNIYPPR<GFTSLLSSKTWILPQP<PHSEGRSEFPSGLLPPSKEPATEHPEPQQET

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_1690 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,