RetrogeneDB ID: retro_ptro_149

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:52658107..52658563(+)
• Located in intron of: ENSPTRG00000000736

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC10
• Ensembl ID: ENSPTRG00000016480
• Aliases: None
• Description: anaphase promoting complex subunit 10 [Source:HGNC Symbol;Acc:24077]

Sequence

>retro_ptro_149
ATGACCACACCAAACAAGACACCTCCTGGTACTGACCCTGAGCAGTTGGAAAAGACTGGAACAGTACGGGAAATTGGGTC
ACAAGCTGTTTGGTCACTCTCATCTTGCAAACCAGGATTTGGAGTGGATCAGTTACGAGCTGACAATCTAGAAACTTATT
GGCAATCAGATGGCTCCCAGCCTCATTTAGGGAACATCCAATTCAGAAGAAAAACAACAGTTAAGACATTATATATTTAT
GCAGACTACAAATCTGATGAAAGCTATACTCTAAGCAAGATTTCAGCCAAAGTAGGAAATAATTTTCACAACCTTCAAGA
AATTCGGCAACTTGAATTGGTGGAACCAAGTGGCTGGATTCACATTCCCTTAACTGATAATCATAGGAAGCCAACTTGGA
CGTTAATGATACAGATTGCTGTTCTAGCCAATCATCAAAATGGAAAAGACACCCAC

Alignment

ORF - retro_ptro_149 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.79 %
• Parental protein coverage: 82.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTPNKTPPGADPKQLERTGTVREIGSQAVWSLSSCKPGFGVDQLRDDNLETYWQSDGSQPHLVNIQFRR
          MTTPNKTPPG.DP.QLE.TGTVREIGSQAVWSLSSCKPGFGVDQLR.DNLETYWQSDGSQPHL.NIQFRR
Retrocopy MTTPNKTPPGTDPEQLEKTGTVREIGSQAVWSLSSCKPGFGVDQLRADNLETYWQSDGSQPHLGNIQFRR

Parental  KTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIRQLELVEPSGWIHVPLTDNHKKPTRTFMIQIA
          KTTVKTL.IYADYKSDESYT.SKIS..VGNNFHNLQEIRQLELVEPSGWIH.PLTDNH.KPT.T.MIQIA
Retrocopy KTTVKTLYIYADYKSDESYTLSKISAKVGNNFHNLQEIRQLELVEPSGWIHIPLTDNHRKPTWTLMIQIA

Parental  VLANHQNGRDTH
          VLANHQNG.DTH
Retrocopy VLANHQNGKDTH

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	0.02 RPM	2.20 RPM
SRP007412_cerebellum	0.07 RPM	1.51 RPM
SRP007412_heart	0.00 RPM	1.92 RPM
SRP007412_kidney	0.00 RPM	2.80 RPM
SRP007412_liver	0.00 RPM	1.90 RPM
SRP007412_testis	0.00 RPM	7.59 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_149 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_149 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_149 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_152
Gorilla gorilla	retro_ggor_241
Pongo abelii	retro_pabe_468
Macaca mulatta	retro_mmul_374
Callithrix jacchus	retro_cjac_2999

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002663	2 retrocopies	retro_cjac_2683, retro_cjac_2999,
Dipodomys ordii	ENSDORG00000016690	1 retrocopy	retro_dord_202,
Homo sapiens	ENSG00000164162	1 retrocopy	retro_hsap_152,
Gorilla gorilla	ENSGGOG00000025091	1 retrocopy	retro_ggor_241,
Myotis lucifugus	ENSMLUG00000008607	1 retrocopy	retro_mluc_1679,
Macaca mulatta	ENSMMUG00000004432	1 retrocopy	retro_mmul_374,
Mus musculus	ENSMUSG00000036977	1 retrocopy	retro_mmus_1511,
Nomascus leucogenys	ENSNLEG00000005453	1 retrocopy	retro_nleu_1498,
Otolemur garnettii	ENSOGAG00000006902	2 retrocopies	retro_ogar_1649, retro_ogar_2510,
Pongo abelii	ENSPPYG00000015096	1 retrocopy	retro_pabe_468,
Pan troglodytes	ENSPTRG00000016480	1 retrocopy	retro_ptro_149 ,
Pteropus vampyrus	ENSPVAG00000013169	2 retrocopies	retro_pvam_1245, retro_pvam_1450,