RetrogeneDB ID: retro_hsap_1037

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:85961655..85961910(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000257855
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDRG1
• Ensembl ID: ENSG00000088356
• Aliases: PDRG1, C20orf126, PDRG
• Description: p53 and DNA-damage regulated 1 [Source:HGNC Symbol;Acc:16119]

Sequence

>retro_hsap_1037
ATGCTGTCACATGATGCAGAGCAAGTTCTGTGGTACCTGTTCGAGGTGGAGGAGCTTGTTGAGGAGGTGCTGGTGGACAA
ACAGCAGATTGTGGATGTGGACACCGAAAGGAATAAAAACCCAGAGGGCCTGAGAGCCCTGCAGAATGGTCTCAGCCTCT
CTGAAGATGTGGTTTGCCTCAGGAACATGTTTGTCAAGATGCCTCACCCTCAGGTGAAGGAAATGATTAAGAAAAATCAG
GATCATCTGGATAAA

Alignment

ORF - retro_hsap_1037 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.42 %
• Parental protein coverage: 64.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSPEAERVLRYLVEVEELAEEVLADKRQIVDLDTKRNQNREGLRALQKDLSLSEDVMVCFGNMFIKMPH
          MLS..AE.VL.YL.EVEEL.EEVL.DK.QIVD.DT.RN.N.EGLRALQ..LSLSEDV.VC..NMF.KMPH
Retrocopy MLSHDAEQVLWYLFEVEELVEEVLVDKQQIVDVDTERNKNPEGLRALQNGLSLSEDV-VCLRNMFVKMPH

Parental  PETKEMIEKDQDHLDK
          P..KEMI.K.QDHLDK
Retrocopy PQVKEMIKKNQDHLDK

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	4.35 RPM
bodymap2_adrenal	0.00 RPM	12.65 RPM
bodymap2_brain	0.00 RPM	9.56 RPM
bodymap2_breast	0.00 RPM	6.71 RPM
bodymap2_colon	0.00 RPM	11.58 RPM
bodymap2_heart	0.00 RPM	5.11 RPM
bodymap2_kidney	0.00 RPM	12.49 RPM
bodymap2_liver	0.00 RPM	6.84 RPM
bodymap2_lung	0.00 RPM	9.48 RPM
bodymap2_lymph_node	0.00 RPM	11.46 RPM
bodymap2_ovary	0.00 RPM	8.93 RPM
bodymap2_prostate	0.00 RPM	18.81 RPM
bodymap2_skeletal_muscle	0.00 RPM	2.91 RPM
bodymap2_testis	0.00 RPM	31.94 RPM
bodymap2_thyroid	0.00 RPM	13.73 RPM
bodymap2_white_blood_cells	0.00 RPM	9.88 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1037 was not detected

EST

No EST(s) were mapped for retro_hsap_1037 retrocopy.

TSS

No TSS is located nearby retro_hsap_1037 retrocopy 5' end.

Lab

retro_hsap_1037 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1037 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_707
Gorilla gorilla	retro_ggor_818
Pongo abelii	retro_pabe_869
Macaca mulatta	retro_mmul_824

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020766	1 retrocopy	retro_cjac_3320,
Homo sapiens	ENSG00000088356	1 retrocopy	retro_hsap_1037 ,
Gorilla gorilla	ENSGGOG00000024924	1 retrocopy	retro_ggor_818,
Macropus eugenii	ENSMEUG00000003915	1 retrocopy	retro_meug_1967,
Myotis lucifugus	ENSMLUG00000007377	1 retrocopy	retro_mluc_348,
Macaca mulatta	ENSMMUG00000000973	1 retrocopy	retro_mmul_824,
Nomascus leucogenys	ENSNLEG00000009712	1 retrocopy	retro_nleu_910,
Oryctolagus cuniculus	ENSOCUG00000016709	1 retrocopy	retro_ocun_1047,
Ochotona princeps	ENSOPRG00000006403	1 retrocopy	retro_opri_630,
Pongo abelii	ENSPPYG00000010897	1 retrocopy	retro_pabe_869,
Pan troglodytes	ENSPTRG00000013368	1 retrocopy	retro_ptro_707,