RetrogeneDB ID: retro_nleu_162

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:681126..682761(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYNCRIP
• Ensembl ID: ENSNLEG00000012879
• Aliases: None
• Description: synaptotagmin binding, cytoplasmic RNA interacting protein [Source:HGNC Symbol;Acc:16918]

Sequence

>retro_nleu_162
ATGGCTACAGAACATGTTAATGGAAATGGTACTGAAGAGCCCATGGATACTAGTTCTGCAGTTGTCCATTCAGAAAATTT
TCAGACGTTGCTTGATGCTGGTTTACCACATAAAATTGCTGAAAAACTAGATGAAATTTATGTTGCAGGGCTAGTTGCAC
ATAGTGATTTAGTTGAAAGAGCTATTGAAGCTTTAAAAGAATTCAATGAAGACGGTGCATTGGCAGTTCTTCAACAGTTA
AAGACAGTGATCTCTCTCATGTTCAGAACAAAAGTGCCTTTTTATGTGGAGACATGAAGACTTATAGGCAGAGAGAAAAA
CAAGGGACCAAAGTAGCAGATTCTAGTAAAGGACCAGATGAGGCAAAAATTAAGGCACTCTTGGAAAGAACAGGCTACAC
ACTTGATGTGACCACTGGACAGAGGAAGTATGGAGGACCACCTCCAGATTCCGTTTATTCAAGTCAGCAGCCTTCTGTTG
GCACTGAGATATTTGTGGGAAAGATCCCAAGAGATGTATTTGAGGATGAACTTGTTCCATTATTTGAGAAAGCTGGATCT
ATATGGGATCATCGTCTAATGATGGGTCCACTCACTGGTCTCAATAGAGGTTATGCGTTTGTCACTTTTTGTACAAAAGA
AGCAGCTCAGGAGGCTGTTAAACTGTATAATAATCATGAAATTCGTTCTGGAAAACACATTGGTGTCTGCATCTCAGTTG
CCAACAATAGGCTTTTTGTGGGCTCTATTCCTAAGAGTAAAACCAAGGAACAGATTCTTGAAGAATTTAGCAAAGTAACA
GAGGGTCTTACAGACGTCATTTTATACCACCAATCGGATGACAAGAAAAGAAAACAGAGGCTTTTGCTTTCTTGAATATG
AAGATCACAAAACAGCTGCCCAGGCAAGGCGTAGTTAATGAGTGGTAAAGTCAAGGTCTGGGGGAATGTTGGAACTGTTG
AATGGGCTGATCCTATGGAAGATCCTGATCCTGAGGTTATGGCAAAGGTAAAAGTGCTGTTTGTACACAACCTTGCCAAT
ACTGTAACAGAAGAGATTTTAGAAAAGGCATTTAGTCAGTTTGGGAAACTGGAACGAGTGAAGAAGTTAAAAGATTATGC
ATTCATTCATTTTGGTGAGTGAGATGGTGCTGTCAAGGCTATGGAAGAAATGAATGGCAAAGACTTGGAGGGAGAAAATA
CTGAAATTGTTTTTGCCAAGCCACCAGATCAGAAAAGGAAAGAAAGAAAAGCTCAGAGGCAAGCAGCAAAAAAATCAAAT
GTATGACGATTACTACTATTATGGTCCATCTTATATGCCCCCTCCAACAAGAGGTCGAGGGTGTGGAGGTAGAGGTGGTT
ATGAATATCCTCCAGATTATTACGGATATGAAGATTATTATGATTATTATGGCTATGATTACCATAACTATTGTGGTGGA
TATGAAGATCCATACTATGGTTATGAAGATTTTCAAGTTGGAGCTAGAGGAAGGCGTGGTAGAGGAGCAAGGGGTGCTGC
TCCATCCAGAGGTCGTGGGGCTGCTCCTCCCCGTGGTAGAGCCGGTTATTCACAGAGAGGAGGTCCTGGATCAGCAAGAG
GCGTTCGAGGTGCGAGAGGAGGTGCCCAACAACAA

Alignment

ORF - retro_nleu_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.54 %
• Parental protein coverage: 96.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATEHVNGNGTEEPMDTTSAVIHSENFQTLLDAGLPQKVAEKLDEIYVAGLVAHSDLDERAIEALKEFNE
          MATEHVNGNGTEEPMDT.SAV.HSENFQTLLDAGLP.K.AEKLDEIYVAGLVAHSDL.ERAIEALKEFNE
Retrocopy MATEHVNGNGTEEPMDTSSAVVHSENFQTLLDAGLPHKIAEKLDEIYVAGLVAHSDLVERAIEALKEFNE

Parental  DGALAVLQQFK-DSDLSHVQNKSAFLCGVMKTYRQREKQGTKVADSSKGPDEAKIKALLERTGYTLDVTT
          DGALAVLQQ.K.DSDLSHVQNKSAFLCG.MKTYRQREKQGTKVADSSKGPDEAKIKALLERTGYTLDVTT
Retrocopy DGALAVLQQLK<DSDLSHVQNKSAFLCGDMKTYRQREKQGTKVADSSKGPDEAKIKALLERTGYTLDVTT

Parental  GQRKYGGPPPDSVYSGQQPSVGTEIFVGKIPRDLFEDELVPLFEKAGPIWDLRLMMDPLTGLNRGYAFVT
          GQRKYGGPPPDSVYS.QQPSVGTEIFVGKIPRD.FEDELVPLFEKAG.IWD.RLMM.PLTGLNRGYAFVT
Retrocopy GQRKYGGPPPDSVYSSQQPSVGTEIFVGKIPRDVFEDELVPLFEKAGSIWDHRLMMGPLTGLNRGYAFVT

Parental  FCTKEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQP
          FCTKEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQ.
Retrocopy FCTKEAAQEAVKLYNNHEIRSGKHIGVCISVANNRLFVGSIPKSKTKEQILEEFSKVTEGLTDVILYHQS

Parental  DDKKK-NRGFCFLEYEDHKTAAQARRR-LMSGKVKVWGNVGTVEWADPIEDPDPEVMAKVKVLFVRNLAN
          DDKK..NRGFCFLEYEDHKTAAQARR..LMSGKVKVWGNVGTVEWADP.EDPDPEVMAKVKVLFV.NLAN
Retrocopy DDKKR>NRGFCFLEYEDHKTAAQARRS<LMSGKVKVWGNVGTVEWADPMEDPDPEVMAKVKVLFVHNLAN

Parental  TVTEEILEKAFSQFGKLERVKKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIEIVFAKPPDQKRKERK
          TVTEEILEKAFSQFGKLERVKKLKDYAFIHF.E.DGAVKAMEEMNGKDLEGEN.EIVFAKPPDQKRKERK
Retrocopy TVTEEILEKAFSQFGKLERVKKLKDYAFIHFGE*DGAVKAMEEMNGKDLEGENTEIVFAKPPDQKRKERK

Parental  AQRQAA-KNQMYDDYYYYGPPHMPPPTRGRGRGGRGGYGYPPDYYGYEDYYDYYGYDYHNYRGGYEDPYY
          AQRQAA.KNQMYDDYYYYGP..MPPPTRGRG.GGRGGY.YPPDYYGYEDYYDYYGYDYHNY.GGYEDPYY
Retrocopy AQRQAA>KNQMYDDYYYYGPSYMPPPTRGRGCGGRGGYEYPPDYYGYEDYYDYYGYDYHNYCGGYEDPYY

Parental  GYEDFQVGARGRGGRGARGAAPSRGRGAAPPRGRAGYSQRGGPGSARGVRGARGGAQQQ
          GYEDFQVGARGR.GRGARGAAPSRGRGAAPPRGRAGYSQRGGPGSARGVRGARGGAQQQ
Retrocopy GYEDFQVGARGRRGRGARGAAPSRGRGAAPPRGRAGYSQRGGPGSARGVRGARGGAQQQ

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_162 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018345	1 retrocopy	retro_dnov_1927,
Homo sapiens	ENSG00000135316	1 retrocopy	retro_hsap_2410,
Macaca mulatta	ENSMMUG00000012575	1 retrocopy	retro_mmul_1843,
Nomascus leucogenys	ENSNLEG00000012879	1 retrocopy	retro_nleu_162 ,
Oryctolagus cuniculus	ENSOCUG00000000601	1 retrocopy	retro_ocun_1683,
Pongo abelii	ENSPPYG00000016819	1 retrocopy	retro_pabe_1775,
Pan troglodytes	ENSPTRG00000018393	1 retrocopy	retro_ptro_1387,
Rattus norvegicus	ENSRNOG00000000204	1 retrocopy	retro_rnor_805,
Sus scrofa	ENSSSCG00000004294	1 retrocopy	retro_sscr_436,
Vicugna pacos	ENSVPAG00000001061	1 retrocopy	retro_vpac_391,