RetrogeneDB ID: retro_nleu_2795

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397431.1:2794355..2795920(-)
• Located in intron of: ENSNLEG00000007910

Retrocopy information

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

Parental gene information

• Parental gene symbol: KLHL12
• Ensembl ID: ENSNLEG00000018103
• Aliases: None
• Description: None

Sequence

>retro_nleu_2795
ATGGGAGGCATATGGCCCCCAAAGACATAATGACAAATACTCATGCTAAATCAATCCTCAATTCAATGGACTCCCTCGGG
AAGAGCAACACCCTCTGTGATGTGACATTGAGAGTAGAGCAGAAAGACTTCCCTGCCCATCAGATTGTGCTGGCTGCCTG
TAGTGATTACTTCTGTGCCATGTTCACTAGTGAGATTTCACAGAAGGGGAAACCTTATGTTGACATCCAAGGTTTGACTG
CCTCTACCATGGAAATTTTATTCGACTTTGTGTACACAGAAACAGTACATGTGACATGGAGAATGTATAAGAACCGCTTC
CTGCAGCCTGTCTGCTTCAGTTGAAAGGTGTGAAACAAGCCTGCTGTGAGTTCTTAGAAAGTCAGTTGGACCCTTCTAAT
TGCCTGGGTATTAGGGATTTTGCTGAAACCCACAATTGTGTTGACCTGACACAAGCAGCTGAGGTTTTTAGCCAGAAGAA
TTTTCCTGAAGTGGTACAGCATGAAGAGTTCATTCTTCGGAGACAAGGAGAGGTGGAAAAGCTAATCGAGTGCGATGAAA
TTCAGATGGATCCTGAAGAACCAGTCTTTGAGGCTGTCCTCAGTTGGGTGAAGCATGTCAAGAAAGGGCAGAAAGAATCC
TTGCCTAACTGGCTACAGTATATGCGGATGCCCCTGCTAACCCTCAGGTATATCACAGATGTAACAGATGCTGAGCCTTT
CATCCGTTGTGGTTTACAACGCGGGGATCTGGTTGATGAAGGAAAGAAGTTTCATCTGAGGCCTGAACTTCAGAGTCAGA
TGCAGGGACCCAGGACAAGGGCTCGCCTAGGAGCCAATGAAGTGCTTTTGGTGGCTGGGGGCTTCAGAAGCCAGCAGTCT
CCCATCGACACAGTAGAGAAATATGACCCCAAGACTCAGGAGTGGAGCTTTTTGCCAAGCATCACTTGTAAGAGACGTTA
TGTGGCCTCAGTGTCCCTACATGACCAGATCTAGGTCATTGGTGGCTATGATAGCCGTTCCTGCCTTAGTTCAGTGGAAT
GTCTAGACTACACAGCAGATGAGGATGGGGTCTGGTATTCTGTGGCCCCTATGAATGTCCAATGAAGTCTTGCTGGATAC
ACCACCCTGGGAGATTTGATCCTATGTCTCTGGAGGCTTTGATGGAAGCAGGTGTCAGATCAGTATGGAGCGGTATGATC
CAAACATTGACCAGTGGAGCATGCTGGGAGATATGCAGACAGCCTGGGAAGGTGCCGGACTCGTAGTGGCCAGTGGAGTG
ATCCACTGTCTAGGAGGATATGACGGCTTGAGTATCTTAAATTCAGTTGAGAAATATGACGCTCATACAGGACACTGGAC
TAATGTTACACCAATGGCCACCAAGTGTTCTGGTGGAGGAGTAGCCCTGCTGAATGACCGTATTTATGTGGTGGGGGGAT
TTGATGGTACAGCCCACCTTTCTTCCGTTGAAGCATACAACATTCGCACTGATTCCTGGACAACTGCCACCAGTATGACC
ACTCCACGATGCTATGTAGGGGCCACAGTGCTTCGGGGGAGAGTA

Alignment

ORF - retro_nleu_2795 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGGI-MAPKDIMTNTHAKSILNSMNSLRKSNTLCDVTLRVEQKDFPAHRIVLAACSDYFCAMFTTELSEK
          MGGI.MAPKDIMTNTHAKSILNSM.SL.KSNTLCDVTLRVEQKDFPAH.IVLAACSDYFCAMFT.E.S.K
Retrocopy MGGI<MAPKDIMTNTHAKSILNSMDSLGKSNTLCDVTLRVEQKDFPAHQIVLAACSDYFCAMFTSEISQK

Parental  GKPYVDIQGLTASTMEILLDFVYTETVHVT-VENVQELLPAACLLQLKGVKQACCEFLESQLDPSNCLGI
          GKPYVDIQGLTASTMEIL.DFVYTETVHVT..ENV.E.LPAACLLQLKGVKQACCEFLESQLDPSNCLGI
Retrocopy GKPYVDIQGLTASTMEILFDFVYTETVHVT<MENV*EPLPAACLLQLKGVKQACCEFLESQLDPSNCLGI

Parental  RDFAETHNCVDLMQAAEVFSQKHFPEVVQHEEFILLSQGEVEKLIKCDEIQVDSEEPVFEAVINWVKHAK
          RDFAETHNCVDL.QAAEVFSQK.FPEVVQHEEFIL..QGEVEKLI.CDEIQ.D.EEPVFEAV..WVKH.K
Retrocopy RDFAETHNCVDLTQAAEVFSQKNFPEVVQHEEFILRRQGEVEKLIECDEIQMDPEEPVFEAVLSWVKHVK

Parental  KEREESLPNLLQYVRMPLLTPRYITDVIDAEPFIRCSLQCRDLVDEAKKFHLRPELRSQMQGPRTRARLG
          K...ESLPN.LQY.RMPLLT.RYITDV.DAEPFIRC.LQ..DLVDE.KKFHLRPEL.SQMQGPRTRARLG
Retrocopy KGQKESLPNWLQYMRMPLLTLRYITDVTDAEPFIRCGLQRGDLVDEGKKFHLRPELQSQMQGPRTRARLG

Parental  ANEVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVEC
          ANEVLLV.GGF.SQQSPID.VEKYDPKTQEWSFLPSIT.KRRYVASVSLHD.I.VIGGYD.RS.LSSVEC
Retrocopy ANEVLLVAGGFRSQQSPIDTVEKYDPKTQEWSFLPSITCKRRYVASVSLHDQI*VIGGYDSRSCLSSVEC

Parental  LDYTADEDGVWYSVAPMNVRRGLAGATTLGDMI-YVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTARE
          LDYTADEDGVWYSVAPMNV...LAG.TTLGD.I.YVSGGFDGSR...SMERYDPNIDQWSMLGDMQTA.E
Retrocopy LDYTADEDGVWYSVAPMNVQ*SLAGYTTLGDLI>YVSGGFDGSRCQISMERYDPNIDQWSMLGDMQTAWE

Parental  GAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNVTPMATKRSGAGVALLNDHIYVVGGFDGTAHL
          GAGLVVASGVI.CLGGYDGL.ILNSVEKYD.HTGHWTNVTPMATK.SG.GVALLND.IYVVGGFDGTAHL
Retrocopy GAGLVVASGVIHCLGGYDGLSILNSVEKYDAHTGHWTNVTPMATKCSGGGVALLNDRIYVVGGFDGTAHL

Parental  SSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRL
          SSVEAYNIRTDSWTT.TSMTTPRCYVGATVLRGR.
Retrocopy SSVEAYNIRTDSWTTATSMTTPRCYVGATVLRGRV

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_2795 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006231	1 retrocopy	retro_cjac_2151,
Dasypus novemcinctus	ENSDNOG00000010436	1 retrocopy	retro_dnov_2190,
Echinops telfairi	ENSETEG00000007800	2 retrocopies	retro_etel_2103, retro_etel_723,
Homo sapiens	ENSG00000117153	1 retrocopy	retro_hsap_2545,
Macaca mulatta	ENSMMUG00000017849	1 retrocopy	retro_mmul_612,
Nomascus leucogenys	ENSNLEG00000018103	1 retrocopy	retro_nleu_2795 ,
Otolemur garnettii	ENSOGAG00000014771	1 retrocopy	retro_ogar_1552,
Pongo abelii	ENSPPYG00000000343	1 retrocopy	retro_pabe_1872,
Pan troglodytes	ENSPTRG00000001861	1 retrocopy	retro_ptro_1483,