RetrogeneDB ID: retro_pabe_1996

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:56578271..56578637(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000029745
• Aliases: None
• Description: None

Sequence

>retro_pabe_1996
AGTGTTCAGACCAAGAAAATTAATGCAAAACTTCCTGATATAGTATGTCAGCGCTATAAAGAAGTTCTTGAGTGTCGTGT
AAAATACAAAAAATACAAACCATTATCAAGCCTAACAAATGTGTTAAATGTTTATAAAAGACAGTGAAGGATTCTTATCA
CACAATGTGTAGACCATGCGCCTGTGAACTTGAAGTTTGCACAAAATGTGGAAGGAAAGAAGACATTGTTATTCTGTTCA
GTAAGGAACCAGAAGAAACAAAATATTGAAGACAATCTAAGTTCCAACCATAGAAGAAGCTGCGGAAGAAATGAAGAAAG
GGATGATAATTTAGATTTTGATGTTGATTTAGAAGACACAGGAGGA

Alignment

ORF - retro_pabe_1996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72. %
• Parental protein coverage: 79.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TIKLQKINAKLHDGVCQRCKEVLEWRVKYSKYKPLS-KPKKCVKCLQKTVKDSYHIMCRPCACELEVCTK
          .....KINAKL.D.VCQR.KEVLE.RVKY.KYKPLS.KP.KCVKCL.KTVKDSYH.MCRPCACELEVCTK
Retrocopy SVQTKKINAKLPDIVCQRYKEVLECRVKYKKYKPLS<KPNKCVKCL*KTVKDSYHTMCRPCACELEVCTK

Parental  CGKKEDIVIPLNKETEKIEH-TENNLSSNHRRSCRRNEESDDDLDFDIDLEDTGG
          CG.KEDIVI...KE.E.......N..S...RRSC.RNEE.DD.LDFD.DLEDTGG
Retrocopy CGRKEDIVILFSKEPEETKY>EDNLSSNH-RRSCGRNEERDDNLDFDVDLEDTGG

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	0.00 RPM	0.28 RPM
SRP007412_cerebellum	0.00 RPM	0.61 RPM
SRP007412_heart	0.15 RPM	0.84 RPM
SRP007412_kidney	0.10 RPM	1.23 RPM
SRP007412_liver	0.00 RPM	0.67 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1996 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1996 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2104
Pan troglodytes	retro_ptro_1543
Macaca mulatta	retro_mmul_988
Callithrix jacchus	retro_cjac_1283

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007254	1 retrocopy	retro_amel_730,
Bos taurus	ENSBTAG00000006831	1 retrocopy	retro_btau_39,
Canis familiaris	ENSCAFG00000001820	1 retrocopy	retro_cfam_2126,
Callithrix jacchus	ENSCJAG00000001441	2 retrocopies	retro_cjac_1283, retro_cjac_1374,
Cavia porcellus	ENSCPOG00000025848	2 retrocopies	retro_cpor_1538, retro_cpor_316,
Felis catus	ENSFCAG00000031942	1 retrocopy	retro_fcat_1955,
Homo sapiens	ENSG00000155621	2 retrocopies	retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus	ENSMLUG00000024309	2 retrocopies	retro_mluc_2449, retro_mluc_2526,
Macaca mulatta	ENSMMUG00000018881	2 retrocopies	retro_mmul_670, retro_mmul_988,
Mustela putorius furo	ENSMPUG00000008971	1 retrocopy	retro_mputfur_1413,
Mus musculus	ENSMUSG00000035171	6 retrocopies	retro_mmus_1049, retro_mmus_2254, retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys	ENSNLEG00000001023	1 retrocopy	retro_nleu_1272,
Oryctolagus cuniculus	ENSOCUG00000024578	2 retrocopies	retro_ocun_703, retro_ocun_766,
Otolemur garnettii	ENSOGAG00000011302	1 retrocopy	retro_ogar_979,
Pongo abelii	ENSPPYG00000029745	2 retrocopies	retro_pabe_1996 , retro_pabe_2397,
Pan troglodytes	ENSPTRG00000021018	2 retrocopies	retro_ptro_1543, retro_ptro_1958,
Rattus norvegicus	ENSRNOG00000027161	5 retrocopies	retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus	ENSSARG00000004523	1 retrocopy	retro_sara_260,
Tupaia belangeri	ENSTBEG00000015556	6 retrocopies	retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,