RetrogeneDB ID: retro_hsap_453

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:149725851..149726170(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000226500
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2D4
• Ensembl ID: ENSG00000078967
• Aliases: UBE2D4, HBUCE1
• Description: ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]

Sequence

>retro_hsap_453
AATGACAGTCCTTGCCAAGGAGGTGTTTTCTTCCTGACCATCCACTTTCCTATGGATTGCCTGTTCAAGCCCCCAAAGGT
TGCTTTCACAACCAAAATTTATCACCCCAATATCAATAGCAATGGCAGCATCTGCTTCAACATCCTATGGTCTCAGTGGT
CTCCAGCATTGACTGTCAAAAGTTCTCTTGTCCATCTGCTCACTGCCCTGCATCCCCAACCTCAATGATCCTCTGGTGCT
AGAGATACCCCACACCTACAAGGCCGACAGAGAGAACTACAACAGACTAGCAAGACAGTGGACAGAAAAATATGCTATG

Alignment

ORF - retro_hsap_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.93 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLL
          NDSP.QGGVFFLTIHFP.D..FKPPKVAFTTKIYHPNINSNGSIC..IL.SQWSPALTV...L......L
Retrocopy NDSPCQGGVFFLTIHFPMDCLFKPPKVAFTTKIYHPNINSNGSICFNILWSQWSPALTVKSSLVHLLTAL

Parental  CDPNP-DDPLVPEIAHTYKADREKYNRLAREWTQKYAM
          ..P.P..DPLV.EI.HTYKADRE.YNRLAR.WT.KYAM
Retrocopy -HPQP>NDPLVLEIPHTYKADRENYNRLARQWTEKYAM

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
bodymap2_adipose	0.00 RPM	4.55 RPM
bodymap2_adrenal	0.00 RPM	6.65 RPM
bodymap2_brain	0.00 RPM	7.74 RPM
bodymap2_breast	0.00 RPM	12.55 RPM
bodymap2_colon	0.00 RPM	7.91 RPM
bodymap2_heart	0.00 RPM	12.94 RPM
bodymap2_kidney	0.00 RPM	7.03 RPM
bodymap2_liver	0.00 RPM	6.38 RPM
bodymap2_lung	0.00 RPM	3.96 RPM
bodymap2_lymph_node	0.00 RPM	9.81 RPM
bodymap2_ovary	0.00 RPM	8.94 RPM
bodymap2_prostate	0.00 RPM	11.79 RPM
bodymap2_skeletal_muscle	0.00 RPM	24.68 RPM
bodymap2_testis	0.00 RPM	6.07 RPM
bodymap2_thyroid	0.00 RPM	7.85 RPM
bodymap2_white_blood_cells	0.00 RPM	4.69 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_453 was not detected

EST

No EST(s) were mapped for retro_hsap_453 retrocopy.

TSS

No TSS is located nearby retro_hsap_453 retrocopy 5' end.

Lab

retro_hsap_453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_453 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_452
Pan troglodytes	retro_ptro_341
Pongo abelii	retro_pabe_3573
Macaca mulatta	retro_mmul_531

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 60 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	ENSG00000072401	2 retrocopies	retro_hsap_4723, retro_hsap_4725,
Homo sapiens	ENSG00000078967	2 retrocopies	retro_hsap_452, retro_hsap_453 ,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Homo sapiens	ENSG00000185651	4 retrocopies	retro_hsap_1094, retro_hsap_1185, retro_hsap_1338, retro_hsap_1960,
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	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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).