RetrogeneDB ID: retro_nleu_2087

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397327.1:10594280..10596173(+)
• 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_2087
ATACAGTCTCTAGAAGAATGAGTCAAAATCCCTCAAATCACTATTAGCTGAACCAAAATGACCTTCAAGAGACTTCAAAT
GAATGAAGAGAAACTGAAGATAGCAATACGAGATGCTTTGAGTGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTT
TGCAAGAAGCTGAAGTATGGAAAGAACAAATGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACAC
GCAGAACGACTTCTAAATGATAAAGAAAATCACATCGAGACTGTGACTGAACGCTTGCTAAAGATCAAAGATCGGGCTGC
TATGCTGGAAGAAGACCTAATGGATGATGGTAACTTGGAATTAGAAATGAACAGTGAATCAGAAGATGGTGCTAACTTAG
ATAATCCTCCAAAACGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAA
AGAAACCAAATGTATATGCAGTTATCTGAAGTTGATAAAACCAAGGAAGAGCTTAGAGAGCATATTAAAAATCTTCAGAC
GGAACAAGCATCTTTGCAGTCAGGAAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGA
CAGAATTATATCAAGAAAATGAAATGAAACTCTGCAGGAAATTAATAGTAGAGGAAAATAACCAGCTAGAGAAAGAGAAA
CTTTCTAAAGTAGATGAAATGATCAGCCATGCCGCTGAAGAGCTGGAGACCTGCAGAAAGCGAACCAAAGATATTGAAGA
AGAATTTGAGAGAACTATTCATTTTTATCAGGGGAAGATTATATACCATGAGAAAAAAGCACACGATAATTGGCTGGCAG
CTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAGCTGAAACAGAGTTT
AAAATTAAACTTTTAGAAAAAGATCCTTACGCACTTGATGTTCCAAATACAGCATTTGGCAGAGAGCATTCCTCATATGG
TCCCTCACCATTGGGCCGGCCTTCATCTGAAACGAGAGCTTTTCTTTATCCTCCAACTTTGTTGGAGGGTTCACTCAGAC
TCTCACCTTTGCTTCCAGGGGGAGGAGGAAGACGCCCAAGAGGCCCAGGGAATCCTCTGGAACACCAGATTACCAAGGAA
AGAGGAGAATCAAGCTGTGATAGGTTAACCGATCCTCACAGGGCTCCTTGTGACACTGGGTTCCTGCCACCTCCATGGGA
ACAGGACGGTAGGATGATGTTTCCCTCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCGCAAAGGCAAGACAGAT
TTATTCTAATTGTGCTAGACGCTCTGGACCAGCAGAACTCGGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATGGGT
CAATGCCTTCAGAAATGGAATCCAGTAGAAATGATACCAAAGATAATCTTGGTAATTTAAATGTGCCTGATCCATCTCTC
CCCGCTGGAAATGAAGCGACTGGCCCTGGCTTTTTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCGTTGTTTCCAATGGA
TATGAGGGGCCCGTTCATGAGCAGAGGACCTCCTTTCCCTCCGCCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAAATT
ATTTTCCACCAAGGGATGTCCCAGGTCCACCACGTGCTCCATTTGCAATGAGAAATGTCTGTCCACCGAGGGGTTTTCCT
CCTTACCTTCCCCCAAGACCTGGATTTCCCCCACCCCGACCCCACATTCTGAAGATAGAGTGAGTTCCCTTCAGGGTGGA
GTCTGCCTTCAAATGAGCCTGCTGCTGAAGATCCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_nleu_2087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.6 %
• Parental protein coverage: 78.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IQSLED-ESKSLKSQVAE-AKMTFKIFQMNEERLKIAIKDALTENSELQESQKQLLQDAEVWKEQVSELN
          IQSLE..ESKSLKS..AE..KMTFK..QMNEE.LKIAI.DAL.ENS.LQESQKQLLQ.AEVWKEQ.SELN
Retrocopy IQSLEE>ESKSLKSLLAE<TKMTFKRLQMNEEKLKIAIRDALSENSQLQESQKQLLQEAEVWKEQMSELN

Parental  KQKVTFEDSTVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPK
          KQK.TFEDS.VHAE..LNDKENHI.T.TERLLK.KD.AAML.ED..DD.NLELEMNSESE.GA.LDNPPK
Retrocopy KQKITFEDSKVHAERLLNDKENHIETVTERLLKIKDRAAMLEEDLMDDGNLELEMNSESEDGANLDNPPK

Parental  GALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDTTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQ
          .ALKKLIHAAKLNASL.TLEGERNQ.Y.QLSEVD.TKEEL.EHIKNLQTEQASLQS.NTHFE.ENQKLQQ
Retrocopy RALKKLIHAAKLNASLTTLEGERNQMYMQLSEVDKTKEELREHIKNLQTEQASLQSGNTHFESENQKLQQ

Parental  KLKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQ
          KLKVMTELYQENEMKL.RKL.VEEN..LEKE.KLSKVDE.ISHA.EELET.RKR.KD.EEE.ERTIH.YQ
Retrocopy KLKVMTELYQENEMKLCRKLIVEENNQLEKE-KLSKVDEMISHAAEELETCRKRTKDIEEEFERTIHFYQ

Parental  GQIISHEKKAHENWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYG
          G.II.HEKKAH.NWLAA..AERNLNDLRKENAHNRQKL.ETE.K..LLEKDPYALDVPNTAFGREHS.YG
Retrocopy GKIIYHEKKAHDNWLAAWTAERNLNDLRKENAHNRQKLAETEFKIKLLEKDPYALDVPNTAFGREHSSYG

Parental  PSPLGWPASETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPS
          PSPLG.P.SETRAFL.PPTLLEG.LRLSPLLPGGGGR..RGPGNP..HQIT.ERGESSCDRLTDPHRAP.
Retrocopy PSPLGRPSSETRAFLYPPTLLEGSLRLSPLLPGGGGRRPRGPGNPLEHQITKERGESSCDRLTDPHRAPC

Parental  DTGSLSPPWEQDRRMMFPPPGQSYPDSALPPQRQDRFC-SNSGRLSGPAELRSFNMPSLDKMDGSMPSEM
          DTG.L.PPWEQD.RMMFP.PGQSYPDSALPPQRQDRF..SN..R.SGPAEL.SFNMPSLDKMDGSMPSEM
Retrocopy DTGFLPPPWEQDGRMMFPSPGQSYPDSALPPQRQDRFI<SNCARRSGPAELGSFNMPSLDKMDGSMPSEM

Parental  EPSRNDSKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFG
          E.SRND.KD.LGNLNVPD.SLPA.NEATGPGF.PPPLAP.RGPLFP.D.RGPF..RGPPFPPPPPG.MFG
Retrocopy ESSRNDTKDNLGNLNVPDPSLPAGNEATGPGFFPPPLAPVRGPLFPMDMRGPFMSRGPPFPPPPPGTMFG

Parental  ASRDYFPPRDFPGPPHAPFAMRNVYPPRGFPPYLP-PRPGFFPPP-PHSEGR-SEFPSGLIPPSNEPATE
          AS..YFPPRD.PGPP.APFAMRNV.PPRGFPPYLP.P.....P.P.PHSE.R.SEFPSG...PSNEPA.E
Retrocopy ASPNYFPPRDVPGPPRAPFAMRNVCPPRGFPPYLP<PKTWISPTPTPHSEDR<SEFPSGWSLPSNEPAAE

Parental  HPERQQET
          .PE.QQET
Retrocopy DPEPQQET

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_2087 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,