RetrogeneDB ID: retro_hsap_1184

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 13:30870283..30870604(+)
• Located in intron of: ENSG00000102781

Retrocopy information

• Ensembl ID: ENSG00000215049
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRDX2
• Ensembl ID: ENSG00000167815
• Aliases: PRDX2, HEL-S-2a, NKEF-B, NKEFB, PRP, PRX2, PRXII, PTX1, TDPX1, TPX1, TSA
• Description: peroxiredoxin 2 [Source:HGNC Symbol;Acc:9353]

Sequence

>retro_hsap_1184
ATGGCCTCAGGTAATGCGTGCATGGGAAAGCCTGCCCCTAACTTCAAGGCCACATCCATGGTGGATGGCGCCTTCAAAGA
GGTGAAGCTGTCAGACTACAAAGGGAAGTACGTGGTCCTCTTTTTCTACCCTCTGGACTTCACTTTTGTGTGCCCCACGG
AGATCACTGCAGTCAGCAGCCATGCCGAGGACTTCCGCAAGCTGGGCTGCGAAGTGCTGGGCATCTTGGTGGACTCTCAG
TTCACCCACCTGGCTTGGATTAACATCCCCCGGAAGGAGGGAGGCTTGGGCCCCCTGAACATCCCCCTGCTTGCTAATGT
G

Alignment

ORF - retro_hsap_1184 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.85 %
• Parental protein coverage: 78.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASGNARIGKPAPDFKATAVVDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAEDFRKLGC
          MASGNA..GKPAP.FKAT..VDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEI.A.S..AEDFRKLGC
Retrocopy MASGNACMGKPAPNFKATSMVDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEITAVSSHAEDFRKLGC

Parental  EVLGVSVDSQFTHLAWINTPRKEGGLGPLNIPLLADV
          EVLG..VDSQFTHLAWIN.PRKEGGLGPLNIPLLA.V
Retrocopy EVLGILVDSQFTHLAWINIPRKEGGLGPLNIPLLANV

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	61.34 RPM
bodymap2_adrenal	0.00 RPM	72.20 RPM
bodymap2_brain	0.00 RPM	101.12 RPM
bodymap2_breast	0.02 RPM	135.78 RPM
bodymap2_colon	0.00 RPM	64.45 RPM
bodymap2_heart	0.00 RPM	129.69 RPM
bodymap2_kidney	0.00 RPM	89.28 RPM
bodymap2_liver	0.00 RPM	69.77 RPM
bodymap2_lung	0.00 RPM	46.91 RPM
bodymap2_lymph_node	0.00 RPM	59.66 RPM
bodymap2_ovary	0.00 RPM	103.79 RPM
bodymap2_prostate	0.00 RPM	85.16 RPM
bodymap2_skeletal_muscle	0.02 RPM	83.63 RPM
bodymap2_testis	0.00 RPM	57.92 RPM
bodymap2_thyroid	0.00 RPM	86.42 RPM
bodymap2_white_blood_cells	0.00 RPM	25.79 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1184 was not detected

EST

No EST(s) were mapped for retro_hsap_1184 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_32454	530 libraries	551 libraries	528 libraries	176 libraries	44 libraries

The graphical summary, for retro_hsap_1184 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1184 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_812
Gorilla gorilla	retro_ggor_923
Pongo abelii	retro_pabe_988

---

Parental genes homology:

Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012307	3 retrocopies	retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris	ENSCAFG00000017163	3 retrocopies	retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis	ENSCING00000003002	1 retrocopy	retro_cint_8,
Callithrix jacchus	ENSCJAG00000004882	4 retrocopies	retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii	ENSDORG00000009005	1 retrocopy	retro_dord_176,
Felis catus	ENSFCAG00000000473	1 retrocopy	retro_fcat_1755,
Homo sapiens	ENSG00000117450	1 retrocopy	retro_hsap_4230,
Homo sapiens	ENSG00000123131	1 retrocopy	retro_hsap_3165,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Homo sapiens	ENSG00000167815	3 retrocopies	retro_hsap_1184 , retro_hsap_3278, retro_hsap_3500,
Gorilla gorilla	ENSGGOG00000025089	3 retrocopies	retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta	ENSMMUG00000005689	2 retrocopies	retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica	ENSMODG00000006978	1 retrocopy	retro_mdom_1770,
Mustela putorius furo	ENSMPUG00000004591	2 retrocopies	retro_mputfur_28, retro_mputfur_660,
Mus musculus	ENSMUSG00000005161	2 retrocopies	retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys	ENSNLEG00000012800	2 retrocopies	retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii	ENSOGAG00000024998	2 retrocopies	retro_ogar_1993, retro_ogar_244,
Pongo abelii	ENSPPYG00000009607	3 retrocopies	retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes	ENSPTRG00000010541	3 retrocopies	retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus	ENSRNOG00000003520	2 retrocopies	retro_rnor_2288, retro_rnor_497,
Sorex araneus	ENSSARG00000000146	1 retrocopy	retro_sara_96,
Sarcophilus harrisii	ENSSHAG00000015596	1 retrocopy	retro_shar_305,
Sus scrofa	ENSSSCG00000013736	2 retrocopies	retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus	ENSSTOG00000025862	1 retrocopy	retro_itri_842,