RetrogeneDB ID: retro_pabe_1987

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:27664006..27664329(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBX1
• Ensembl ID: ENSPPYG00000011861
• Aliases: None
• Description: ring-box 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:9928]

Sequence

>retro_pabe_1987
ATGGTGGCAGCGATGGAAGAGGGTACCCTGAGCAGCACCAATGACAGTGTGGGCAAGAATGGCTTTAAAGTGAAAAAGTG
GAATGCAGTAGCCCTCTGGGCTGGGATATTGTGCTTGGTAACTGTGCCATCTGCAGGAACCACATTATGGATCTTTGCAT
AGAATGTCAAGCTAACCAAGTGTCTGCTACTTCTGAAGAGTATACCATCTTATGGGGCATTTGTAACCATGCTTTTCACT
TCCACTGCATCTGTCACTGGCTCAAAACACCACAGGTATGTCCATTGGACAACAAAGAGTGAGAATTCCAAAAGTATGGG
CAC

Alignment

ORF - retro_pabe_1987 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAAMDVDTPSGTNSGAGKKRFEVKKWNAVALWA-WDIVVDNCAICRNHIMDLCIECQANQASATSEECT
          M.AAM...T.S.TN...GK..F.VKKWNAVALWA.WDIV..NCAICRNHIMDLCIECQANQ.SATSEE.T
Retrocopy MVAAMEEGTLSSTNDSVGKNGFKVKKWNAVALWA<WDIVLGNCAICRNHIMDLCIECQANQVSATSEEYT

Parental  VAWGVCNHAFHFHCISRWLKTRQVCPLDNREWEFQKYGH
          ..WG.CNHAFHFHCI..WLKT.QVCPLDN.E.EFQKYGH
Retrocopy ILWGICNHAFHFHCICHWLKTPQVCPLDNKE*EFQKYGH

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	40.97 RPM
SRP007412_cerebellum	0.00 RPM	24.93 RPM
SRP007412_heart	0.00 RPM	24.44 RPM
SRP007412_kidney	0.00 RPM	40.34 RPM
SRP007412_liver	0.00 RPM	26.26 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1987 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1987 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1987 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000030225	2 retrocopies	retro_btau_1415, retro_btau_61,
Callithrix jacchus	ENSCJAG00000004763	3 retrocopies	retro_cjac_1267, retro_cjac_1955, retro_cjac_1962,
Dasypus novemcinctus	ENSDNOG00000007595	1 retrocopy	retro_dnov_433,
Homo sapiens	ENSG00000100387	1 retrocopy	retro_hsap_2118,
Loxodonta africana	ENSLAFG00000008795	1 retrocopy	retro_lafr_943,
Microcebus murinus	ENSMICG00000008019	1 retrocopy	retro_mmur_750,
Myotis lucifugus	ENSMLUG00000007815	4 retrocopies	retro_mluc_1259, retro_mluc_1712, retro_mluc_20, retro_mluc_244,
Macaca mulatta	ENSMMUG00000012642	3 retrocopies	retro_mmul_702, retro_mmul_974, retro_mmul_996,
Monodelphis domestica	ENSMODG00000013054	1 retrocopy	retro_mdom_626,
Mus musculus	ENSMUSG00000022400	1 retrocopy	retro_mmus_1633,
Nomascus leucogenys	ENSNLEG00000015436	1 retrocopy	retro_nleu_1956,
Ochotona princeps	ENSOPRG00000006728	2 retrocopies	retro_opri_410, retro_opri_649,
Pongo abelii	ENSPPYG00000011861	2 retrocopies	retro_pabe_1986, retro_pabe_1987 ,
Pongo abelii	ENSPPYG00000014167	2 retrocopies	retro_pabe_1446, retro_pabe_2228,
Pan troglodytes	ENSPTRG00000014417	1 retrocopy	retro_ptro_1550,
Rattus norvegicus	ENSRNOG00000019214	2 retrocopies	retro_rnor_1890, retro_rnor_2724,
Ictidomys tridecemlineatus	ENSSTOG00000015580	1 retrocopy	retro_itri_888,
Tupaia belangeri	ENSTBEG00000009043	4 retrocopies	retro_tbel_1175, retro_tbel_3306, retro_tbel_3756, retro_tbel_3805,
Tursiops truncatus	ENSTTRG00000012018	2 retrocopies	retro_ttru_1419, retro_ttru_583,
Vicugna pacos	ENSVPAG00000004894	2 retrocopies	retro_vpac_207, retro_vpac_502,
Drosophila melanogaster	FBgn0025638	1 retrocopy	retro_dmel_55,