RetrogeneDB ID: retro_nleu_2600

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397379.1:2129850..2131937(+)
• 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_2600
TCATCTTTAGAGGACGCCAGCTTTGAGAAGGCGGCAGCAGAAGCACGAAGTTTGGAGGCAACCTGTGAAAAGCTGAACAG
GTCCAGTTCTGAACTTGAGCATGAAATCCTCTGCCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTCAACAAA
ATGAATTGATGGAGGATATTTCAAAAAGGATACAGCCTCTAGCAGATAAGTCAAAATCCCTCAAATCACAAGTAGCTGAA
GCCAAAATGATCTTCAAGGGATTTCAAATGACTGAAAAACAACTGAAGATAGCAATAAAAGATGCTTTGAATGAAAATTC
TCAACTTCAGGAAAGCCAGAAACAGCTTTTCCAAGAAGCTGAAGTATGGAACGAACAAGTGAGTGAACTTAATAAACAGA
AAATAACATGTGAAGACTCCAAAGTACATGCAGAACAAGTTCTAAATGATAAAGCAAATCGCATCAAGACTCTGACTGAA
CGCTTGCTAAAGATGAAAGATTGGGCTGCTAGGCTTAGAGAAGACGTAACGGATGATGATAACTTAGAATTAGAAGTGAA
CAGTGAATCAGAAGATGGTGCTTACTTAGATGATCCTCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAA
ATGCTTCTTTAAAAACCTTAGAAGGAGAAAGAAACCAAATTTACATCCAGCTATCTGAAATTGATAAAACAAAGGAAGAG
CTTACAGAGCATATTAAAAATCTTCGGACTGAACAAGCATCTTTGCAGTCAGAAAACACACATTTTGAAAGTGAGAATCA
GAAGCTTCAACAGAAACTTAAAGTAATGACTGAATCATATCAAGAAAATGAAATGAAACTCTACAGGAAATTAACAGTAG
AGGAAAATAACCAGTTAGAGAAAGAAGAGAAACTTTCTAAGGTAGACAAAAAGATCAGCCATGCCACTAAAGAGCTAGAG
ACCTACAGACAGCAAGCCAAAGATCTTGAAGAAGAATTGGAGATAACTATTCATTATTATCAACAGCAGGTTATTTCCCA
TGGGAAAAAAGCACATCATAATTGGTTGGCAGCTTGGACTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTC
ACAACAGACAAAAATTAACTGAAACAGAGTTTAAATTTGAACTTTTAGAAAAAGGTCCTTATGTACTTGATGTTCCAAAT
ACAGCATTTGGCAGAGAGCATTCCCCATATGGTCCTTCATCATTGGGTTGGCCTTCATCTGAAACGAGAGCTTTTCTCTC
TCCCGCAACTCTATTGGAGGGTCCACTCAGACTCTCACCTTTGCCTCCAGGGGGAGAAGGAAGAGGCTCAAGAGGCCCAG
GGAATCCTCTGGACCATCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGAGAGGTTAACCGATCCTCACAGGTCTCCT
TCTGACACTGGGTCCCTGTCACCTCCGAGGGAACAGGACCATAGGATGATGTTTCCCCCACCAGGGCAATCATATCTTGA
TTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATTCTAACTCTGGTAGACTGTCTGGAGCAGCAGAACTCAGAAGTT
TTAATATGCCTCCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAAATGACACCAAAGATGAT
CTTGGTAATTTAAATATGCCTGATTCATCTCTTCCTGCTGAAAATGAAGCAACTGGTCCTGGCTTTGTTCCTCCACCTCT
TGCCCCAATCAGAGGCCCATTGTTTCCGGTGGATACAAGGGGCCTGTTCATGAGAAGAGGACCTCCTTTCCCCCCACCTC
CTCCAGGAACCAGGTTTGGAGCTTCTTGAGGTTATTGTCCACCAAGGGATTTCCCAGGTCCGCCACACGCTCCATTTGCA
ATGAGAAACGTCTATCCACCGAGGGGTTTTCCTCCTTACCTTCCTCTCAAGACCTGGATTTTTCCCCCCAACCCCCACAT
TCTGAAGGTTTAAGTGAGTTCCCTTCAGGGCTGATTCTGCCTTCAAATGAGCCTGCTACTGAACATCCAAAACCGCAGCA
AGACACC

Alignment

ORF - retro_nleu_2600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.51 %
• Parental protein coverage: 85.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASFEKEATEAQSLEVKNQMATCEKLNRSNSELEDEILCLEKELKEEKCKHSEQDELMADISKRIQSLEDE
          .S.E....E....E.....ATCEKLNRS.SELE.EILCLEKELKEEK.KHS.Q.ELM.DISKRIQ.L.D.
Retrocopy SSLEDASFEKAAAEARSLEATCEKLNRSSSELEHEILCLEKELKEEKSKHSQQNELMEDISKRIQPLADK

Parental  SKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALTENSELQESQKQLLQDAEVWKEQVSELNKQKVTFEDS
          SKSLKSQVAEAKM.FK.FQM.E..LKIAIKDAL.ENS.LQESQKQL.Q.AEVW.EQVSELNKQK.T.EDS
Retrocopy SKSLKSQVAEAKMIFKGFQMTEKQLKIAIKDALNENSQLQESQKQLFQEAEVWNEQVSELNKQKITCEDS

Parental  TVHAEQVLNDKENHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHA
          .VHAEQVLNDK.N.IKTLTERLLKMKDWAA.L.ED.TDDDNLELE.NSESE.GAYLD.PPKGALKKLIHA
Retrocopy KVHAEQVLNDKANRIKTLTERLLKMKDWAARLREDVTDDDNLELEVNSESEDGAYLDDPPKGALKKLIHA

Parental  AKLNASLKTLEGERNQIYIQLSEVDTTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELY
          AKLNASLKTLEGERNQIYIQLSE.D.TKEELTEHIKNL.TEQASLQSENTHFE.ENQKLQQKLKVMTE.Y
Retrocopy AKLNASLKTLEGERNQIYIQLSEIDKTKEELTEHIKNLRTEQASLQSENTHFESENQKLQQKLKVMTESY

Parental  QENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKK
          QENEMKL.RKLTVEEN..LEKEEKLSKVD.KISHAT.ELETYR..AKDLEEELE.TIH.YQ.Q.ISH.KK
Retrocopy QENEMKLYRKLTVEENNQLEKEEKLSKVDKKISHATKELETYRQQAKDLEEELEITIHYYQQQVISHGKK

Parental  AHENWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPAS
          AH.NWLAA..AERNLNDLRKENAHNRQKLTETE.KFELLEK.PY.LDVPNTAFGREHSPYGPS.LGWP.S
Retrocopy AHHNWLAAWTAERNLNDLRKENAHNRQKLTETEFKFELLEKGPYVLDVPNTAFGREHSPYGPSSLGWPSS

Parental  ETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPVDHQITNERGESSCDRLTDPHRAPSDTGSLSPPW
          ETRAFLSP.TLLEGPLRLSPL.PGG.GRGSRGPGNP.DHQIT.ERGESSC.RLTDPHR.PSDTGSLSPP.
Retrocopy ETRAFLSPATLLEGPLRLSPLPPGGEGRGSRGPGNPLDHQITKERGESSCERLTDPHRSPSDTGSLSPPR

Parental  EQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMEPSRNDSKDD
          EQD.RMMFPPPGQSY.DSALPPQRQDRF.SNSGRLSG.AELRSFNMP.LDKMDGSMPSEME.SRND.KDD
Retrocopy EQDHRMMFPPPGQSYLDSALPPQRQDRFYSNSGRLSGAAELRSFNMPPLDKMDGSMPSEMESSRNDTKDD

Parental  LGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGPFLRRGPPFPPPPPGAMFGASRDYFPPRD
          LGNLN.PDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRG.F.RRGPPFPPPPPG..FGAS..Y.PPRD
Retrocopy LGNLNMPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGLFMRRGPPFPPPPPGTRFGAS*GYCPPRD

Parental  FPGPPHAPFAMRNVYPPRGFPPYLP-PRPGFFPP-PPHSEGRSEFPSGLIPPSNEPATEHPERQQET
          FPGPPHAPFAMRNVYPPRGFPPYLP..RPGFFPP.PPHSEG.SEFPSGLI.PSNEPATEHP..QQ.T
Retrocopy FPGPPHAPFAMRNVYPPRGFPPYLP>SRPGFFPP>PPHSEGLSEFPSGLILPSNEPATEHPKPQQDT

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_2600 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,