RetrogeneDB ID: retro_nleu_2951

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397511.1:157254..158814(-)
• 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_2951
GAGAAGACAATGGATGATGGTAACTTATAATTAGAAGTGAACAGTGAATGGGAAGATGGTGCTCACTTAGATGATCCCTC
AAAAGGAGCTTCGAAGAAGCTGATTCATGCTGCTAAGTTAAATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAGCCAAA
TTTATAGTCAGTTATCTGAAGTTGATAAAACAAAGTAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTGAACAAGCA
TCTTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAGTAATGACTGAATTATA
TAAAGAAAATGAAATGAAACTCTACAGGAAATTAATAGTAGAGGAAAATTACCGGTTAGAGAAAGAAGATAAACTTTCCA
AAGTAGACGAAATTATCAGCCATGCCACTAAAGAGCTGGAGACCTACAGACAGCGAGCCAAAGATCTTGAAGAATTTGAG
AGAACTATTCATTTTTATCAAAGGAAGATTATTTCCCATGAGAAAAAAGCACATCATAACTGGTTGGCAGCTTGGGCTGT
TGAAAGAAACCTGGACGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAGCTGAAACAGAGTATAAAATAAAAC
TTCCAAAAAAAGATCCTTATGCGCTTGATGTTCCAAATACGGCCTTTGGCAGAGAGCATTCCCCACATGGTCCCTCACCA
TTGGGTCGGCCTTCACCTGAAACGAGAGCTTTTCTCTCTCCCGCAACTTTGTTGGAGGGTCCACTCAGACTCTCACCTTT
GTCTCCTGGGGGAGAAGGAAGAGGCTCAAGAGGCCCAGGGAATCCTCTGGACCATCAGATTACCAATGAAAGGGGAGAAT
CAAGCTGTGAGAGGTTAATCCATCCTCACAGGTCTCCTTCTGACACTGGGTCCCTGTCACCTCCGTGGGAACAGGACTGT
AGGATGATGTTTCCACCACCAGGACAGTCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAA
CTCTGCTAGACTTTCTGGACCAGCAGAACTCAGAAGTTTTAATATGCCTCCTTTGGATAAAATGGGTGGGTCAATGCCTT
CAGAAATGGAATCCAGTAGAAATGACACCAAAGATGATCTTGGTAATTTAAATATGCCTGATTCTTCTCTCCCTGCTGAA
AATGAAGCAACTGACCCTGGCTTTGTTCCTCCACCTCTTGCCCCAATCAGAGGTCCATTGTTTCGAGTGGATACAAGGGA
CCGGTTCATGAGAAGAGGACCTCCTTTCCCCCACCTCCTCCAGGAACCAGGTTTGGAGCTTCTCCAGGTTATTTTCCACC
AAGGGATTTCCCAGGTCCACGACATGCTTCGTTTGCAATGAGAAACGTCTACCCACCGAGGGGTTTTCCTCCTTACCCTC
CCTCAAGACCTGGATTTCCCCCCACCCCCACATTCTGAAGGTTGAAGTGAGTTCCCTTCAGGGCTCAGTCCGCCTTCAAA
TGAGCCTGCTACTGAACATCCAGAACCACAGCAAGACACC

Alignment

ORF - retro_nleu_2951 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.73 %
• Parental protein coverage: 64.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDTTKEELTE
          E...DD.NL.LE.NSE.E.GA.LD.P.KGA.KKLIHAAKLNASLKTLEGER.QIY.QLSEVD.TK.ELTE
Retrocopy EKTMDDGNL*LEVNSEWEDGAHLDDPSKGASKKLIHAAKLNASLKTLEGERSQIYSQLSEVDKTK*ELTE

Parental  HIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKIS
          HIKNLQTEQASLQSENTHFE.ENQKLQQKLKVMTELY.ENEMKL.RKL.VEENYRLEKE.KLSKVDE.IS
Retrocopy HIKNLQTEQASLQSENTHFESENQKLQQKLKVMTELYKENEMKLYRKLIVEENYRLEKEDKLSKVDEIIS

Parental  HATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHENWLAARNAERNLNDLRKENAHNRQKLTETE
          HAT.ELETYR.RAKDLEE..ERTIH.YQ..IISHEKKAH.NWLAA...ERNL.DLRKENAHNRQKL.ETE
Retrocopy HATKELETYRQRAKDLEE-FERTIHFYQRKIISHEKKAHHNWLAAWAVERNLDDLRKENAHNRQKLAETE

Parental  LKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPASETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGP
          .K..L..KDPYALDVPNTAFGREHSP.GPSPLG.P..ETRAFLSP.TLLEGPLRLSPL.PGG.GRGSRGP
Retrocopy YKIKLPKKDPYALDVPNTAFGREHSPHGPSPLGRPSPETRAFLSPATLLEGPLRLSPLSPGGEGRGSRGP

Parental  GNPVDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSG
          GNP.DHQITNERGESSC.RL..PHR.PSDTGSLSPPWEQD.RMMFPPPGQSYPDSALPPQRQDRF.SNS.
Retrocopy GNPLDHQITNERGESSCERLIHPHRSPSDTGSLSPPWEQDCRMMFPPPGQSYPDSALPPQRQDRFYSNSA

Parental  RLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGP
          RLSGPAELRSFNMP.LDKM.GSMPSEME.SRND.KDDLGNLN.PDSSLPAENEAT.PGFVPPPLAPIRGP
Retrocopy RLSGPAELRSFNMPPLDKMGGSMPSEMESSRNDTKDDLGNLNMPDSSLPAENEATDPGFVPPPLAPIRGP

Parental  LFPVDTRGPFLRRGPP-FPPPPPGAMFGASRDYFPPRDFPGPPHAPFAMRNVYPPRGFPPYLPPRPGFFP
          LF.VDTR..F.RRGPP.FPPPPPG..FGAS..YFPPRDFPGP.HA.FAMRNVYPPRGFPPY.P.RPG.FP
Retrocopy LFRVDTRDRFMRRGPP<FPPPPPGTRFGASPGYFPPRDFPGPRHASFAMRNVYPPRGFPPYPPSRPG-FP

Parental  P-PPHSEGRSEFPSGLIPPSNEPATEHPERQQET
          P.PPHSEG.SEFPSGL.PPSNEPATEHPE.QQ.T
Retrocopy P>PPHSEG*SEFPSGLSPPSNEPATEHPEPQQDT

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_2951 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,