RetrogeneDB ID: retro_nleu_3023

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397589.1:79219..80120(-)
• Located in intron of: ENSNLEG00000000934

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSNLEG00000015009
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_nleu_3023
GCGGCAGCAGCGGCGGGAGGCTGGGGCTGTGGGTGGTCGGGCCTCCGGGCCAGGGTGCTGGCGCCATCGTGTGCCTGGGG
CCAGTGGGGAGGCCGGGGAGGGGGCCCCGGGGGGCGCAGGGGACTACGGGAACGGCCTGTAGTCTGAGGAACTGAAGCCT
GAGGAGCTGCCGCTGGACCCCGAGCCGGAACCCGAGCCCGAAGAGGAGCCGCCCCGGCCCTGCGCCCCCACCCCCACGGG
AGCTCCGGGTCTGGTTCGGGAGCCCCTGGCAGCCAAGAGGAGGAGGAGGAGCCGGGACTGGTCGAGGGTGACCTGGAGGA
CGGCGCCATTGAGGATCCAGAGCTGGAAGCTATCAAAGCTCGAGTTAGGGAGATGGAGGAAGAAGCTGAGAAGCTAAAGG
AGCTACACAACGAGGTAGAGAAGTAGATGATTATGAGTCCACCTCCAGGCAATGCTGGCCCAGTGATCACGTCATTGAGA
AGATGGAGGCCGATGCCCGTTCCATCTATGTTGGCACTGTGGACTATGGTGCAACAGCAGAAAAGCTGGAAGCTCACTTT
CATGGCTGTGGTTCAGTCAACCGTGTTACCATACTCTGTGACAAATTTAGTGGCCATCCCAAAGGGTTTGCATATATAGA
GTTCTCAGACAAAGAGTCAGTGAGGACTTCCTTGGCCTTAGATGACTCCCTACTTAGAGGAAGGCAAATAAAGGTGATCC
CAAAACGAACCAACAGACCAGGAATCAGCACAACAGAGTGGGGTTTTCCACGAGCCCACTACCGCGCCCGACCACCAACT
ACAACAGTTCCCTCTCTCGATTCTACAGCGGTTTTAACAGCAGGCCCCGGGGTCGCATCTACAGGGGCCGGGCTAGAGCG
ACATCATGGTACTCCCCTTAC

Alignment

ORF - retro_nleu_3023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.45 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AAAAAA-AAGAAGRGSGPGR-RRHLPGAGGEAGEGGPGGRRGYGNGE-SEELEPEELLLEPEPEPEPEEE
          AAAAA..A....GR.SGPG..R...P................YGNG..SEEL.PEEL.L.PEPEPEPEEE
Retrocopy AAAAAG>AGAVGGRASGPGCWRHRVPXXXXXXXXXXXXXXXXYGNGL*SEELKPEELPLDPEPEPEPEEE

Parental  PPRPRAPPGAPGPG-PGSGAPGSQEEEEEPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNE
          PPRP.AP.....PG..GSGAPGSQEEEEEPGLVEGD..DGAIEDPELEAIKARVREMEEEAEKLKEL.NE
Retrocopy PPRPCAPTPTGAPG<SGSGAPGSQEEEEEPGLVEGDLEDGAIEDPELEAIKARVREMEEEAEKLKELHNE

Parental  VEKQMNMSPPPGNAGPVIMS-IEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGH
          VEK.M.MS.PP............EKMEADARSIYVG.VDYGATAE.LEAHFHGCGSVNRVTILCDKFSGH
Retrocopy VEK*MIMS-PPPGNAGPVIT<VIEKMEADARSIYVGTVDYGATAEKLEAHFHGCGSVNRVTILCDKFSGH

Parental  PKGFAYIEFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRAR-TTNYNSSRSRF
          PKGFAYIEFSDKESVRTSLALD.SL.RGRQIKVIPKRTNRPGISTT..GFPRA.YRAR.TTNYNSS.SRF
Retrocopy PKGFAYIEFSDKESVRTSLALDDSLLRGRQIKVIPKRTNRPGISTTEWGFPRAHYRAR<TTNYNSSLSRF

Parental  YSGFNSRPRGRVYRGRARATSWYSPY
          YSGFNSRPRGR.YRGRARATSWYSPY
Retrocopy YSGFNSRPRGRIYRGRARATSWYSPY

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_3023 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006884	1 retrocopy	retro_btau_693,
Callithrix jacchus	ENSCJAG00000007960	4 retrocopies	retro_cjac_1263, retro_cjac_2291, retro_cjac_3278, retro_cjac_3836,
Dipodomys ordii	ENSDORG00000002873	1 retrocopy	retro_dord_606,
Homo sapiens	ENSG00000100836	1 retrocopy	retro_hsap_4855,
Gorilla gorilla	ENSGGOG00000022683	2 retrocopies	retro_ggor_1454, retro_ggor_3030,
Mustela putorius furo	ENSMPUG00000006775	1 retrocopy	retro_mputfur_496,
Mus musculus	ENSMUSG00000022194	1 retrocopy	retro_mmus_403,
Nomascus leucogenys	ENSNLEG00000015009	2 retrocopies	retro_nleu_2066, retro_nleu_3023 ,
Otolemur garnettii	ENSOGAG00000008710	1 retrocopy	retro_ogar_797,
Pongo abelii	ENSPPYG00000005663	2 retrocopies	retro_pabe_1645, retro_pabe_3773,
Pan troglodytes	ENSPTRG00000006168	2 retrocopies	retro_ptro_1339, retro_ptro_3232,
Sus scrofa	ENSSSCG00000002023	1 retrocopy	retro_sscr_625,