RetrogeneDB ID: retro_nleu_1812

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397311.1:8502953..8503622(+)
• Located in intron of: ENSNLEG00000008924

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LRRC57
• Ensembl ID: ENSNLEG00000004485
• Aliases: None
• Description: None

Sequence

>retro_nleu_1812
ATAGGAGACGGTGCCCGCGGTACTCAAGTGGAATGGGCACACTAAACTGGTGTCTCCCAGTGTAAGGACCGTGGGCTGAC
CAAGTTCTCCTTAGAATTGTATACACTAATGAGCAATCCCAGGACCATCGATTTGTCCAACAACAAGATGGAGAACCTAC
CACTTTTGCTGATACATAAGTTCACTCTGCTGAAGAACCTCTCCCTGAACAACATAAACTGGTCTGCCTAATGAGATTAT
GCAATCCTAAAAAAATTCTAGAGATGCTACGCCTAAACAGCAGTCACCTGAGAGAGCTGCCATCTACCTTTGGGCAACTC
TCTACCCTCAAGACCCTGAGCCTCTCTGGGAACCAACTAGGAGCGCTATCACCCAACTTTGTAGCCTAGGCCACCAGATG
CAGTGGATCTTTCCAAGAACCAGATTTGAAGTATACCTGACATAGTAGGAGAGCTGCAGGTCATCAAACTCATCCTCAAC
TGGAAGAAGATATCTCAGGTCTCAATAAAGATATCTGGCTGTCCTTGCCTTAAAATTCTTCACCTGGAAGAGAACTGTCC
TGAGCTCAGCATGCTTTCACAGAGCATATGCAGTGATTGCCAGATCTGCCCACTTGATATGGAAGGCAATCTTTTTAAAA
TAAACTTCAGTAAGTACATGGAGAAGTTC

Alignment

ORF - retro_nleu_1812 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.94 %
• Parental protein coverage: 93.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGNSALRAHVETAQKTGVFQLQDRGLTEFPADLQKLTSNLRTIDLSNNKIESLPPLLIGKFTLLKSLSLN
          .G..A....VE.A..TGV.Q..DRGLT.F...L..L.SN.RTIDLSNNK.E.LP.LLI.KFTLLK...L.
Retrocopy IGDGARGTQVEWAH*TGVSQCKDRGLTKFSLELYTLMSNPRTIDLSNNKMENLPLLLIHKFTLLKN--LS

Parental  SNKL-TVLPDEI-CNLKK-LETLSLNNNHLRELPSTFGQLSALKTLSLSGNQLGALPP-QLCSLRHL-DV
          .N...T.LP.EI.CN.KK.LE.L.LN..HLRELPSTFGQLS.LKTLSLSGNQLGAL.P.QLCSL.H..D.
Retrocopy LNNI>TGLPNEI>CNPKKILEMLRLNSSHLRELPSTFGQLSTLKTLSLSGNQLGALSP<QLCSLGHQ<DA

Parental  MDLSKNQIRSIPDTVGELQVIELNLNQNQISQISVKISCCPRLKILRLEENCLELSMLPQSILSDSQICL
          .DLSKNQI.SIPD.VGELQVI.L.LN...ISQ.S.KIS.CP.LKIL.LEENC.ELSML.QSI.SD.QIC.
Retrocopy VDLSKNQI*SIPDIVGELQVIKLILNWKKISQVSIKISGCPCLKILHLEENCPELSMLSQSICSDCQICP

Parental  LAVEGNLFEIKKLRELEGY
          L..EGNLF.I......E..
Retrocopy LDMEGNLFKINFSKYMEKF

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_1812 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006482	1 retrocopy	retro_chof_2306,
Callithrix jacchus	ENSCJAG00000002991	1 retrocopy	retro_cjac_2819,
Homo sapiens	ENSG00000180979	1 retrocopy	retro_hsap_2163,
Gorilla gorilla	ENSGGOG00000009597	1 retrocopy	retro_ggor_1718,
Loxodonta africana	ENSLAFG00000005465	2 retrocopies	retro_lafr_1027, retro_lafr_767,
Macaca mulatta	ENSMMUG00000001544	1 retrocopy	retro_mmul_901,
Nomascus leucogenys	ENSNLEG00000004485	1 retrocopy	retro_nleu_1812 ,
Nomascus leucogenys	ENSNLEG00000012444	1 retrocopy	retro_nleu_462,
Otolemur garnettii	ENSOGAG00000007751	1 retrocopy	retro_ogar_3437,
Pan troglodytes	ENSPTRG00000006976	2 retrocopies	retro_ptro_1649, retro_ptro_1650,
Rattus norvegicus	ENSRNOG00000009143	1 retrocopy	retro_rnor_796,
Rattus norvegicus	ENSRNOG00000048310	1 retrocopy	retro_rnor_1732,