RetrogeneDB ID: retro_nleu_688

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397270.1:6176223..6177830(+)
• 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_688
CTCCTTGAATGCTTGCTAAAGATCAAAGATCGGGCTGCTATGCTGGAAGAAGACCTAATGGATGATCGTAACTTGGAATT
AGAAGTGAATAGTGAATCAGAAGATGGTGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAAACTGCTTCATGCTG
CTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACCAAATTTATATTCAGTTATCTGAAGTTGATAAAACC
AAGGAAGAGCTTAGAGAGCATATTAAAAAATCTTCAGATGGAACAAGCATCTTTGTAGTTGGAAAACACATATTTTGAAA
GTGAGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGACAGAATTATATCAAGAAAATGAAATGAAACTCTACAGGAAA
TTAATAGTAGAGGAAAATAACCATCTAGAGAAAGAGAAACTTTCTAAAGTAGATGAAATGATCAGCCATGCCGCTGAAGA
GCTGGAGACCTGCAGAAAGCGAGCCAAAGATCTTGAAGAAGAATTTAAAAGATCTATTCATTTTTATCAAGGGAATATTA
TATACCATGAGAAAAAAGCACATGATAATCGTTTGGCAGCACGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAA
AGTGCTCACAACAGACAAAAATTAGCTGAAACAGAGTTTAAAATTAAGCTTTTAGAAAAAGATCCTTATGCACTTGATGT
TCCAAATACAGCATTTGGCAGAGAGCATTCCTCATATGGTCCCTCACCATTGGGTTGGCCTTCATCTGAAATGAGAGCTT
TTCTCTATCCTCCAACTTTGTTGGAGGGTCCACTCAGACTCTCACCTCTGCTTCCAGGGGGAGGAGGAAGAGGCCCAAGA
GGCCCAGGGAATCCTCTGGACCATCAGATACCAAGGAAAGAGGAGAATCAAGCTGTGATAGGTTAACCGATCCTCACAGG
GCTCCTTGTGACTTCCTGCCACCCCCGTGGGAACAGGACCTTAGGATGATGTCTCCTCCACCAGGACAATCATATCCTGA
TTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAATTGTGCTAGACGCTCTGGACCAGCAGAACTCAGAAGTT
TTAATATGCCTTCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGATACCAAAGATAAT
CTTGGTAATTTATATGTGCCTGATCCATCTCTCCCCGCTGGAAATGAAGCGACTGGCCCTGGCTTTGTTCCTCCACCTCT
TGCTCCAATCAGAGGTCCGTTGTTTCCAGTGGATATGAGGGGCCCGTTCATGAGAAGAGGACCTCCTTTCCCTCCACCTC
CTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTCCACCAAGGGATGTCCCAGGTCCACCACGTGCTCCATTTGCA
ATGAGAAATGTCTATCCACCGAGGGGATTTCCTCCTTACCTTCCCCCAAGACCTGGATTTCCCCCACCCCCGACCCCACA
TTCTGAAGATAGAGTGAGTTCCCTTCATGGTTGAGTCTGCCTTCAAATGAGCCTGCTACTGAAGATCCAGAACCACAGCA
AGAAACC

Alignment

ORF - retro_nleu_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.87 %
• Parental protein coverage: 66.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEGERNQI
          L.E.LLK.KD.AAML.ED..DD.NLELE.NSESE.GAYLDNPPKGALKKL.HAAKLNASL.TLEGERNQI
Retrocopy LLECLLKIKDRAAMLEEDLMDDRNLELEVNSESEDGAYLDNPPKGALKKLLHAAKLNASLTTLEGERNQI

Parental  YIQLSEVDTTKEELTEHIK-NLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLTVEEN
          YIQLSEVD.TKEEL.EHIK.NLQ.EQASL..ENT.FE.ENQKLQQKLKVMTELYQENEMKL.RKL.VEEN
Retrocopy YIQLSEVDKTKEELREHIK>NLQMEQASL*LENTYFESENQKLQQKLKVMTELYQENEMKLYRKLIVEEN

Parental  YRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHENWLAARNAERNLN
          ..LEKE.KLSKVDE.ISHA.EELET.RKRAKDLEEE..R.IH.YQG.II.HEKKAH.N.LAAR.AERNLN
Retrocopy NHLEKE-KLSKVDEMISHAAEELETCRKRAKDLEEEFKRSIHFYQGNIIYHEKKAHDNRLAARTAERNLN

Parental  DLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPASETRAFLSPPTLLEGPL
          DLRKE.AHNRQKL.ETE.K..LLEKDPYALDVPNTAFGREHS.YGPSPLGWP.SE.RAFL.PPTLLEGPL
Retrocopy DLRKESAHNRQKLAETEFKIKLLEKDPYALDVPNTAFGREHSSYGPSPLGWPSSEMRAFLYPPTLLEGPL

Parental  RLSPLLPGGGGRGSRGPGNPVDHQI-TNERGESSCDRLTDPHRAPSDTGSLSPPWEQDRRMMFPPPGQSY
          RLSPLLPGGGGRG.RGPGNP.DHQI.T.ERGESSCDRLTDPHRAP.D...L.PPWEQD.RMM.PPPGQSY
Retrocopy RLSPLLPGGGGRGPRGPGNPLDHQI<TKERGESSCDRLTDPHRAPCDF--LPPPWEQDLRMMSPPPGQSY

Parental  PDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSKDDLGNLNVPDSSLPAEN
          PDSALPPQRQDRF.SN..R.SGPAELRSFNMPSLDKMDGSMPSEME.SRND.KD.LGNL.VPD.SLPA.N
Retrocopy PDSALPPQRQDRFYSNCARRSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDNLGNLYVPDPSLPAGN

Parental  EATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPHAPFAMRNVY
          EATGPGFVPPPLAPIRGPLFPVD.RGPF.RRGPPFPPPPPG.MFGAS.DYFPPRD.PGPP.APFAMRNVY
Retrocopy EATGPGFVPPPLAPIRGPLFPVDMRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDVPGPPRAPFAMRNVY

Parental  PPRGFPPYLPPRPGFFPPP-PHSEGR-SEFPSGLIPPSNEPATEHPERQQET
          PPRGFPPYLPPRPGF.PPP.PHSE.R.SEFPS.L..PSNEPATE.PE.QQET
Retrocopy PPRGFPPYLPPRPGFPPPPTPHSEDR<SEFPSWLSLPSNEPATEDPEPQQET

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_688 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,