RetrogeneDB ID: retro_pabe_3573

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:11644370..11644691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSPPYG00000029727
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_pabe_3573
AATGACAGTCCTTGCCAAGGAGGTGTTTTCTTCCTGACCATCCACTTTCCTACGGATTGCCTGTTCAAGCCCCCAAAGGA
TGCTTTCACAACCAAAATTTATCACCCCAATATCAATAGCAATGGCAGCATCTGCTTCGACATCCTATGGTCTCAGTGGT
CTCCAGCATTGACTGTGTCAAAAGATCTCTTGTCCATCTGCTCACTGCCCTGCATCCCCAACCTCAATGATCCTCTGGTG
CTAGAGATAGCCCACACCTACAAGGCCGACAGAGAGAACTACAACAGACTAGCAAGACAGTGGACAGAAAAATATGCTAT
G

Alignment

ORF - retro_pabe_3573 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 62.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLL
          NDSP.QGGVFFLTIHFPTD..FKPPK.AFTTKIYHPNINSNGSIC.DIL.SQWSPALTVSK.LLSICSL.
Retrocopy NDSPCQGGVFFLTIHFPTDCLFKPPKDAFTTKIYHPNINSNGSICFDILWSQWSPALTVSKDLLSICSLP

Parental  CDPNPDDPLVPEIAHTYKADREKYNRLAREWTQKYAI
          C.PN..DPLV.EIAHTYKADRE.YNRLAR.WT.KYA.
Retrocopy CIPNLNDPLVLEIAHTYKADRENYNRLARQWTEKYAM

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	23.39 RPM
SRP007412_cerebellum	0.00 RPM	23.96 RPM
SRP007412_heart	0.00 RPM	14.12 RPM
SRP007412_kidney	0.00 RPM	18.73 RPM
SRP007412_liver	0.00 RPM	13.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3573 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3573 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_453
Homo sapiens	retro_hsap_452
Pan troglodytes	retro_ptro_341
Macaca mulatta	retro_mmul_531

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003997	1 retrocopy	retro_btau_1261,
Callithrix jacchus	ENSCJAG00000007875	4 retrocopies	retro_cjac_1660, retro_cjac_3666, retro_cjac_3882, retro_cjac_925,
Dipodomys ordii	ENSDORG00000006888	5 retrocopies	retro_dord_104, retro_dord_345, retro_dord_408, retro_dord_743, retro_dord_760,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453,
Gorilla gorilla	ENSGGOG00000003378	3 retrocopies	retro_ggor_1843, retro_ggor_2936, retro_ggor_436,
Myotis lucifugus	ENSMLUG00000011919	3 retrocopies	retro_mluc_1826, retro_mluc_1827, retro_mluc_594,
Macaca mulatta	ENSMMUG00000002410	5 retrocopies	retro_mmul_1067, retro_mmul_1937, retro_mmul_2514, retro_mmul_2515, retro_mmul_531,
Nomascus leucogenys	ENSNLEG00000003364	3 retrocopies	retro_nleu_54, retro_nleu_876, retro_nleu_90,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Pongo abelii	ENSPPYG00000011602	1 retrocopy	retro_pabe_99,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Pongo abelii	ENSPPYG00000014967	1 retrocopy	retro_pabe_91,
Pongo abelii	ENSPPYG00000015844	6 retrocopies	retro_pabe_1016, retro_pabe_1164, retro_pabe_1257, retro_pabe_2330, retro_pabe_30, retro_pabe_3670,
Pongo abelii	ENSPPYG00000029727	1 retrocopy	retro_pabe_3573 ,
Sus scrofa	ENSSSCG00000016722	2 retrocopies	retro_sscr_671, retro_sscr_79,
Tupaia belangeri	ENSTBEG00000003691	9 retrocopies	retro_tbel_1273, retro_tbel_2535, retro_tbel_2782, retro_tbel_307, retro_tbel_367, retro_tbel_37, retro_tbel_4118, retro_tbel_4163, retro_tbel_4312,
Tarsius syrichta	ENSTSYG00000000595	14 retrocopies	retro_tsyr_1007, retro_tsyr_1145, retro_tsyr_1162, retro_tsyr_1314, retro_tsyr_1392, retro_tsyr_1415, retro_tsyr_1677, retro_tsyr_1694, retro_tsyr_1859, retro_tsyr_683, retro_tsyr_789, retro_tsyr_836, retro_tsyr_838, retro_tsyr_919,