RetrogeneDB ID: retro_nleu_847

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:40229120..40229863(-)
• Located in intron of: ENSNLEG00000017432

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPI1
• Ensembl ID: ENSNLEG00000004821
• Aliases: None
• Description: triosephosphate isomerase 1 [Source:HGNC Symbol;Acc:12009]

Sequence

>retro_nleu_847
GCTGACACTGAACTTCAGCGCCTCAGCTCCAGCGCCATGGCACCCTCCAGGAAGTTCTTCACGGGGGAGCTGGAAGATGA
ACGGGTGGAAGAAGAGTCTTGGGGAGCCCATTGACACTGAACATGACCAAGGTGCCAGCTGACACCGAGGTGGTTTGCTC
TCCCCCCACTGCCTATATCGACTTCACCCAGCAGAAGCTAGATCCCAAGATTGCTGTGCCTGCACAGAACGGCTACAAAG
TGACTAATGGGGCCTTCACTGGGTAGATCAGCCCTGGCATAATCACAGACTGCGGAGCTACTTGGGTGGTCCTGGGGCAC
TCAGAGAGAAGGCATGTCTTTGGGTAGTCAGATGAACTGATTGAGCAGAAAGTGGCCCATGCTCTGGCAGAGGGACTTGG
AGTAATCGCCTGCATTGGGAAGAAGCTACATGCAAGGGAAGCTGGCATCACTGAGAAGGTTGTTTTTGAGCAGACAAAGG
TCATCACAGATAAGGTGAAAGACTGGAGCAAGGTCATCCTGGCTGATAAGCCTGTGTGGGACATTGGTACTAGCAAGACT
GCAACACCCCAACAGGCCCAGGAAGTACACAAGAAGCTCCAAGGATGGCTTAAATCCAATGTCTCTGATGCAGTGGCTCA
GAGCACCCATATCATTTATGAAGGCTCTGTGACCAGGGTAACCTGCAAGGAGCTGGTCAGCCAGCCTGACGTGGATGGCT
TCCTCCTGGGTGGTTCTTCCCTC

Alignment

ORF - retro_nleu_847 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.6 %
• Parental protein coverage: 68.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADTDLQRLGSSAMAPSRKFFV-GGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLD
          ADT.LQRL.SSAMAPSRKFF..GG.....G....LG....TLN..KVPADTEVVC.PPTAYIDF..QKLD
Retrocopy ADTELQRLSSSAMAPSRKFFT<GGAGR*TGGRRVLGSPL-TLNMTKVPADTEVVCSPPTAYIDFTQQKLD

Parental  PKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIAC
          PKIAV.AQN.YKVTNGAFTG.ISPG.I.DCGATWVVLGHSERRHVFG.SDELI.QKVAHALAEGLGVIAC
Retrocopy PKIAVPAQNGYKVTNGAFTG*ISPGIITDCGATWVVLGHSERRHVFG*SDELIEQKVAHALAEGLGVIAC

Parental  IGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGWLKSNV
          IG.KL..REAGITEKVVFEQTKVI.D.VKDWSKV.LA..PVW.IGT.KTATPQQAQEVH.KL.GWLKSNV
Retrocopy IGKKLHAREAGITEKVVFEQTKVITDKVKDWSKVILADKPVWDIGTSKTATPQQAQEVHKKLQGWLKSNV

Parental  SDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVADADL
          SDAVAQST.IIY.GSVT..TCKEL.SQPDVDGFL.....L
Retrocopy SDAVAQSTHIIYEGSVTRVTCKELVSQPDVDGFLLGGSSL

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_847 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190, retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847 ,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,