RetrogeneDB ID: retro_nleu_3112

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL399617.1:6379..7526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CLK2
• Ensembl ID: ENSNLEG00000012062
• Aliases: None
• Description: None

Sequence

>retro_nleu_3112
AGCAGTAGTGACCGGACACGACGGCGCCGGCGAGAGGACAGCTACCATGTCCAGAGGAGGCGCAGCCGGACATTTAGCTG
CTCGTCTTCGCAGCACAGCAGCCGGAAAGCCAAGAGCGTAGAGGACGACGCTGAGGGCCACCTCATCTACCACGTCGGGG
CCTGGCTACAAGAGCGATATGAAATCGTTAGCACCTTAGGAAAGGGGACCTTCGGCCGAGTTGTACAATGTGTTGACCAT
CGCAGGAGTGGGGCTCGAGTTGCCCTGAAGATCATTAAGAATGTGGGGAAGTGTAAGGAGGCAGCTCAACTTGAGATCAA
CGTGCTGGAGAAAATCAACAAGAAAGACCCTGACAAGAACCTCTGTGTCCAGATGTTTGACTGGTTTGACTACCATGGCC
ATGTGTGTATCTCCTTGGAGCTTCTGGGCCTTAGCACCTTCGATTTCCTCAAAGACAACAACTACCTGCCCTACCCCATC
CACCAAGTGCGCCACATGGCCTTCCAGCTGTGCCAGGCTGTCAAGTTCCTCCATGATAACAAGCTGACACATACAGACCT
CAAGCCTGAAAATATTCTGTTTGTGAATTCAGACTATGAGCTCACCTACAACCTAGAGAAGAAGTGACATGAGCACAGTG
TGAAGAGCACAGCTGTGCGGGTGGGAGACTTTGGCAGTGCCACCTTTGACCATGAGCACCACAGCACCATTGTCTCCACT
CACCATTACCGAGCACCAGAGGTCATCCCTGAGTTGGGCTGGTCACAGCCTTGTGATGTGTGGAGTATAGGCTGCATCAT
CTTTGAGTACTATGTGGGCTTCACCCTCTTCCAGACCCATGATAACAGAGAGCATCTAGCCATGATGGAAAGGATCTTGG
GTCCTATCCCTTCCCGGATGATCCGAAAGACAAGAAAACAGAAATATTTTTACCGGGGTCGCCTGGATTGGGATGAGAAC
ACATCAGCTGGGCGCTATGTTCGTGAGAACTGCAAACCGCTGCGGCAGTATCTGACCTCAGAGGCAGAGGACATCACCAG
CCTTCGATCTGATTGAAAGCATGCTAGAGTATGAACCAGCTAAGCGGCTGACCTTGGGTGAAGCCCTTCAGCATCCTTTC
TTCGCCCACCTTTGGGCTGAGCCACCC

Alignment

ORF - retro_nleu_3112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.16 %
• Parental protein coverage: 76.75 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSSYRSQRSSRR-KHRRRRRRSRTFSRSSSQHSSRRAKSVEDDAEGHLIYHVGDWLQERYEIVSTLGEGT
          .SS.R..R..R.......RRRSRTFS.SSSQHSSR.AKSVEDDAEGHLIYHVG.WLQERYEIVSTLG.GT
Retrocopy SSSDRTRRRRREDSYHVQRRRSRTFSCSSSQHSSRKAKSVEDDAEGHLIYHVGAWLQERYEIVSTLGKGT

Parental  FGRVVQCVDHRRGGARVALKIIKNVEKYKEAARLEINVLEKINEKDPDNKNLCVQMFDWFDYHGHMCISF
          FGRVVQCVDHRR.GARVALKIIKNV.K.KEAA.LEINVLEKIN.KDPD.KNLCVQMFDWFDYHGH.CIS.
Retrocopy FGRVVQCVDHRRSGARVALKIIKNVGKCKEAAQLEINVLEKINKKDPD-KNLCVQMFDWFDYHGHVCISL

Parental  ELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKKR
          ELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKK.
Retrocopy ELLGLSTFDFLKDNNYLPYPIHQVRHMAFQLCQAVKFLHDNKLTHTDLKPENILFVNSDYELTYNLEKK*

Parental  DERSVKSTAVRVVDFGSATFDHEHHSTIVSTRHYRAPEVILELGWSQPCDVWSIGCIIFEYYVGFTLFQT
          .E.SVKSTAVRV.DFGSATFDHEHHSTIVST.HYRAPEVI.ELGWSQPCDVWSIGCIIFEYYVGFTLFQT
Retrocopy HEHSVKSTAVRVGDFGSATFDHEHHSTIVSTHHYRAPEVIPELGWSQPCDVWSIGCIIFEYYVGFTLFQT

Parental  HDNREHLAMMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLRRYLTSEAEE-HHQ-
          HDNREHLAMMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLR.YLTSEAE..HHQ.
Retrocopy HDNREHLAMMERILGPIPSRMIRKTRKQKYFYRGRLDWDENTSAGRYVRENCKPLRQYLTSEAED<HHQ<

Parental  LFDLIESMLEYEPAKRLTLGEALQHPFFARLRAEPP
          .FDLIESMLEYEPAKRLTLGEALQHPFFA.L.AEPP
Retrocopy AFDLIESMLEYEPAKRLTLGEALQHPFFAHLWAEPP

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_3112 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000176444	1 retrocopy	retro_hsap_3827,
Gorilla gorilla	ENSGGOG00000009438	1 retrocopy	retro_ggor_2575,
Nomascus leucogenys	ENSNLEG00000011291	1 retrocopy	retro_nleu_1453,
Nomascus leucogenys	ENSNLEG00000012062	2 retrocopies	retro_nleu_2126, retro_nleu_3112 ,
Pan troglodytes	ENSPTRG00000001419	1 retrocopy	retro_ptro_2604,
Tupaia belangeri	ENSTBEG00000000216	2 retrocopies	retro_tbel_4081, retro_tbel_4274,