RetrogeneDB ID: retro_pabe_468

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:177497771..177498209(-)
• Located in intron of: ENSPPYG00000001352

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC10
• Ensembl ID: ENSPPYG00000015096
• Aliases: None
• Description: anaphase promoting complex subunit 10 [Source:HGNC Symbol;Acc:24077]

Sequence

>retro_pabe_468
TTTGGAGTGGATCAGTTACGAGATGACAATCTAGAAACTTATTGGCAATCAGATGGCTCCCAGCCTCATTTAGTGAACAT
CCAATTCAGAAGAAAAACAACAGTTAAGACATTATATATTTATGCAGACTACAAATCTGATGAAAGCTATACTCCAAGCA
AGATTTCAGCCAAAGTAGGAAATAATTTTCACAACCTTCAAGAAATTTGGCAACTTGAATTGGTGGAACGAAGTGGCTGG
ATTCATATTCCCTTAACTGATAATCATAGGAAGCCAACTTGCACGTTAATGATACAGATTGCTGTTCTAGCCAGTCATCA
GAATGGAAAAGACACCCATATGAGACAAATTAAAATATACACACCGGTAGAAGAGAGCACCATTGGTAAATTTCCTAGAT
GTACAACTGTAGATTTCATGATGTATTGTTCAATAAGG

Alignment

ORF - retro_pabe_468 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.41 %
• Parental protein coverage: 90.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKTLCIYADYKSDESYTPSKISVRVGNNFHNLQEIR
          FGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKTL.IYADYKSDESYTPSKIS..VGNNFHNLQEI.
Retrocopy FGVDQLRDDNLETYWQSDGSQPHLVNIQFRRKTTVKTLYIYADYKSDESYTPSKISAKVGNNFHNLQEIW

Parental  QLELVEPSGWIHVPLTDNHKKPTRTFMIQIAVLANHQNGRDTHMRQIKIYTPVEESSIGKFPRCTTIDFM
          QLELVE.SGWIH.PLTDNH.KPT.T.MIQIAVLA.HQNG.DTHMRQIKIYTPVEES.IGKFPRCTT.DFM
Retrocopy QLELVERSGWIHIPLTDNHRKPTCTLMIQIAVLASHQNGKDTHMRQIKIYTPVEESTIGKFPRCTTVDFM

Parental  MYRSIR
          MY.SIR
Retrocopy MYCSIR

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	0.44 RPM	1.55 RPM
SRP007412_cerebellum	0.36 RPM	3.89 RPM
SRP007412_heart	0.45 RPM	1.96 RPM
SRP007412_kidney	0.50 RPM	2.92 RPM
SRP007412_liver	0.46 RPM	2.45 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_468 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_468 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_468 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_152
Pan troglodytes	retro_ptro_149
Gorilla gorilla	retro_ggor_241
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,