RetrogeneDB ID: retro_ptro_3232

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:71145770..71146660(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PABPN1
• Ensembl ID: ENSPTRG00000006168
• Aliases: None
• Description: poly(A) binding protein, nuclear 1 [Source:HGNC Symbol;Acc:8565]

Sequence

>retro_ptro_3232
GCGGCTGGGGCTGCAGGCGGTCGGGCCTCCGGGTCAGGGCGGTGGCGCCATCTTGTGCCTGGGGCCGGTGGGGAGGCCGG
GGAGGGGGCCCCGGGGGGCGTAGGGGACTACGGGAACGGCCTGGAGTCTGAGGAACTGGAGCCTGAGGAGCTGCCGCTGG
ACCCCGAGCCGGAGCCCAAGCCTGAAGAGGAGCCTCCCTGGCCTTGCGCCCCCCACCCCCACGGGAGCTCCAGGCCTGGT
TCGGGAGCCCCTGGCAGCCAAGAGGAGGAGGAGGAGCCATGACTGGTCGAGGGTGACCCGGAAGACAGCGCCATTGAGGA
TCCGGAGCTGGAAGCTATCAAAGCTCGAGTTAGGGAGATGGAGGAAGAAGCTGAGAAGCTAAAGGAGCTACAGAACGAGG
TAGAGAAGCAGATGAGTATGAGTCCACCTCCAGGAAATCCTGGCCCAGTGATCATGTCATTGAGGAGAAGATGGAGGCCG
ATGCCCGTTCCATCTATGTTGGCAATGTTGACTATGGTGCAACAGCAGAAGAGCTGGAAGCTCACTTTCATGGCTGTGGT
TCAGTCAACCGTGTTACCATACTCTGTGACCAATTTAGTGGCCATTCCAAAGGGTTTGCATATATAGAGTTCTCAGACAA
AGAGTCAGTGAGGACTTCCCTGGCCTTAGATGACTCCCTATTTAGAGGAAGGCAAATCAAGGTGATCCCAAAATGAACCA
ACAGACCAGGAATCAGCACAACAGATCGGGGTTTTCCACGAGCCTGCTACCATGCCCGGACCACCAACTACAACAGTTCC
CTCTCTCAATTCCACAGTGGTTTTAACAGCAGGCCCCGGGGTCACGTCTACAGAGGCCAGGCTAGAGCGACATCATGGTA
CTCCCCTTAC

Alignment

ORF - retro_ptro_3232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.2 %
• Parental protein coverage: 97.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAGAAGGRGSGPGRRRHLVPGAGGEAGEGAPGGAGDYGNGLESEELEPEELLLEPEPEPEPEEEPPRPRA
          AAGAAGGR.SG.GR.RHLVP................YGNG............L.PEPEP.PEEEPP.P.A
Retrocopy AAGAAGGRASGSGRWRHLVPXXXXXXXXXXXXXXXXYGNGXXXXXXXXXXXPLDPEPEPKPEEEPPWPCA

Parental  PPGAPGPGPGSGAPGSQEEEEEPGLVEGDPGDGAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMNM
          P.......PGSGAPGSQEEEEEP.LVEGDP.D.AIEDPELEAIKARVREMEEEAEKLKELQNEVEKQM.M
Retrocopy PHPHGSSRPGSGAPGSQEEEEEP*LVEGDPEDSAIEDPELEAIKARVREMEEEAEKLKELQNEVEKQMSM

Parental  SPPPGNAGPVIMS-IEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYI
          SPPPGN.GPVIMS.IEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCD.FSGH.KGFAYI
Retrocopy SPPPGNPGPVIMS<IEEKMEADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDQFSGHSKGFAYI

Parental  EFSDKESVRTSLALDESLFRGRQIKVIPKRTNRPGISTTDRGFPRARYRARTTNYNSSRSRFYSGFNSRP
          EFSDKESVRTSLALD.SLFRGRQIKVIPK.TNRPGISTTDRGFPRA.Y.ARTTNYNSS.S.F.SGFNSRP
Retrocopy EFSDKESVRTSLALDDSLFRGRQIKVIPK*TNRPGISTTDRGFPRACYHARTTNYNSSLSQFHSGFNSRP

Parental  RGRVYRGRARATSWYSPY
          RG.VYRG.ARATSWYSPY
Retrocopy RGHVYRGQARATSWYSPY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.16 RPM	158.83 RPM
SRP007412_cerebellum	0.32 RPM	166.73 RPM
SRP007412_heart	0.06 RPM	49.81 RPM
SRP007412_kidney	0.18 RPM	125.97 RPM
SRP007412_liver	0.23 RPM	90.58 RPM
SRP007412_testis	0.32 RPM	140.05 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3232 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3232 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3232 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4855
Gorilla gorilla	retro_ggor_3030
Macaca mulatta	retro_mmul_2594

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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,