RetrogeneDB ID: retro_hsap_217

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 1:146649692..146651203(+)
• Located in intron of: ENSG00000237188

Retrocopy information

• Ensembl ID: ENSG00000180867
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDIA3
• Ensembl ID: ENSG00000167004
• Aliases: PDIA3, ER60, ERp57, ERp60, ERp61, GRP57, GRP58, HEL-S-269, HEL-S-93n, HsT17083, P58, PI-PLC
• Description: protein disulfide isomerase family A, member 3 [Source:HGNC Symbol;Acc:4606]

Sequence

>retro_hsap_217
ATGTGCCTCCGCCGCCCAGCGCTGTTCCCGGGCGTGGCGCTGCTTCTCGCCGCGGCCCGCCTCGCGGCTGCCTCCGACGT
GCTAGGACTCAGGGACGACAACTTGGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCG
CCCCCTGGTGTGGACACTGCAAGAGACTTGCTCCTGAGTATGAAGCTGCAGCTACCAGATTAAAAGGAATAGTCCCATTA
GCAAAGGCTGATTGCACTGCCAACACTAACACCTGTAATAAATATGGAGTCAGTGGATATCCAACCCTGAATATGTTTAG
AGATGGTGAAGAAGCAGGTGCTTATGATGGACCTAGGACTGCTGATGGAATTGTCAGCCACCTGAAGAAGCAGGCAGGCC
CAGCTTCAGTGCCTCTCAGGACTGAGGAAGAATTTAAGAAATTCATTAGTGATAAAGATGCCTCTATAGTAGGTTTTTTC
GATGATTCATTCAGTGAAGCTCACTCCGAGTTCCTAAAAGCAGCCAGCAACTTGAGGGATAACTACCGATTTGCACATAC
GAATGTTGAGTCTCTGGTGAACGAGTATGATGATAACGGAGATGGTATCATCTTATTTCGTCCTTCACATCTCACTAACA
AGTTGGAGGACAAGACTGTGGCATATACAGTGCAAAAAATGACCAGTGGCAAAATTAAAAAGTTTATCCAGGAAAACATT
TTTGGTATCTGCCCTCACATGACAGAAGACAATAAAGATTTGATACAGGGCAAGGACTTACTTATTGCTTACTATGATGT
GGACTATGAAAAGAATGCTAAAGGTTCCAACTACTGGAGAAACAGGGTAATGATGGTGGCAAAGAAATTCCTGGATGCTG
GGCACAAACTCAACTTTGCTGTAGCTAGCCGCAAAACCTTTAGCCATGAACTTTCTGATTTTGGCTTGGAGAGCACTGCT
GGAGAGATTCCTGTTGTTGCTATCAGAACTGCTAAAGGAGAGAAGTTTGTCATGCAGGAGGATTTCTCGCGTGATGGGAA
TGCTCTGGAGAGGTTCCTGCAGGATTACTTTGATGGCAATCTGAAGAGATACCTGAAGTCTGAACCTATCCCAGAGAGCA
ATGATGGGCCTGTGAAGGTAGTGGTAGCAGAGAATTTTGATGAAATAGTGAATAATGAAAATAAAGATGTGCTGATTGAA
TTTTATGCCCCTTGGTGTGGTCACTGTAAGAACCTGGAGCCCAAGTATAAAGAACTTGGCGAGAAGCTCAGCAAAGACCT
GAATATCGTCATAGCCAAGATGGATGCCACAGCCAATGATGTGCCTTCTCCATATGAAGTCAGAGTTTTCCTACCATATA
CTTCTCTCCAGCCAACAAGAAGCTAAATCCAAAGAAATATGAAGGTGGCCATGAATTAAGTGATTTTATTAGCTATCTAC
AACGAGAAGCTACAAACCCCCCTGTAATTCAAGAAGAAAAACCCAAGAAGAAGAAGGCACAGGAGGATCTC

Alignment

ORF - retro_hsap_217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLRRLALFPGVALLLAAARLAAASDVLELTDDNFESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
          M.LRR.ALFPGVALLLAAARLAAASDVL.L.DDN.ESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
Retrocopy MCLRRPALFPGVALLLAAARLAAASDVLGLRDDNLESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA

Parental  ATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
          ATRLKGIVPLAK.DCTANTNTCNKYGVSGYPTL..FRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
Retrocopy ATRLKGIVPLAKADCTANTNTCNKYGVSGYPTLNMFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR

Parental  TEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSH
          TEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNG.GIILFRPSH
Retrocopy TEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGDGIILFRPSH

Parental  LTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWR
          LTNK.EDKTVAYT.QKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWR
Retrocopy LTNKLEDKTVAYTVQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWR

Parental  NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALE
          NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQE.FSRDG.ALE
Retrocopy NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEDFSRDGNALE

Parental  RFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELG
          RFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELG
Retrocopy RFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEFYAPWCGHCKNLEPKYKELG

Parental  EKLSKDPNIVIAKMDATANDVPSPYEVR-GFPTIYFSPANKKLNPKKYEGGRELSDFISYLQREATNPPV
          EKLSKD.NIVIAKMDATANDVPSPYEVR..FPTIYFSPANKKLNPKKYEGG.ELSDFISYLQREATNPPV
Retrocopy EKLSKDLNIVIAKMDATANDVPSPYEVR<SFPTIYFSPANKKLNPKKYEGGHELSDFISYLQREATNPPV

Parental  IQEEKPKKKKKAQEDL
          IQEEKP.KKKKAQEDL
Retrocopy IQEEKP-KKKKAQEDL

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	1.51 RPM	277.58 RPM
bodymap2_adrenal	2.72 RPM	400.05 RPM
bodymap2_brain	2.60 RPM	137.36 RPM
bodymap2_breast	2.39 RPM	259.40 RPM
bodymap2_colon	3.36 RPM	368.29 RPM
bodymap2_heart	1.72 RPM	116.12 RPM
bodymap2_kidney	3.16 RPM	480.53 RPM
bodymap2_liver	1.39 RPM	765.35 RPM
bodymap2_lung	0.63 RPM	392.23 RPM
bodymap2_lymph_node	1.81 RPM	262.43 RPM
bodymap2_ovary	4.78 RPM	435.43 RPM
bodymap2_prostate	2.63 RPM	295.98 RPM
bodymap2_skeletal_muscle	0.69 RPM	71.24 RPM
bodymap2_testis	3.47 RPM	439.43 RPM
bodymap2_thyroid	3.33 RPM	807.67 RPM
bodymap2_white_blood_cells	1.95 RPM	322.72 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_hsap_217 in 2 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF002DBO	POLR2A	1:146649546..146649930
ENCFF002DBP	POLR2A	1:146649548..146649878

EST

No EST(s) were mapped for retro_hsap_217 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_81887	555 libraries	751 libraries	489 libraries	30 libraries	4 libraries

The graphical summary, for retro_hsap_217 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_217 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_217 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_331
Gorilla gorilla	retro_ggor_287

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000167004	1 retrocopy	retro_hsap_217 ,
Gorilla gorilla	ENSGGOG00000023440	1 retrocopy	retro_ggor_287,
Myotis lucifugus	ENSMLUG00000009380	1 retrocopy	retro_mluc_2352,
Otolemur garnettii	ENSOGAG00000004298	1 retrocopy	retro_ogar_1750,
Procavia capensis	ENSPCAG00000012905	1 retrocopy	retro_pcap_409,
Pan troglodytes	ENSPTRG00000007002	1 retrocopy	retro_ptro_331,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	2.03 RPM
CEU_NA11843	1.93 RPM
CEU_NA11930	3.16 RPM
CEU_NA12004	2.17 RPM
CEU_NA12400	1.86 RPM
CEU_NA12751	1.63 RPM
CEU_NA12760	2.56 RPM
CEU_NA12827	2.26 RPM
CEU_NA12872	1.55 RPM
CEU_NA12873	1.18 RPM
FIN_HG00183	4.69 RPM
FIN_HG00277	1.59 RPM
FIN_HG00315	2.90 RPM
FIN_HG00321	1.39 RPM
FIN_HG00328	1.99 RPM
FIN_HG00338	1.66 RPM
FIN_HG00349	2.79 RPM
FIN_HG00375	2.27 RPM
FIN_HG00377	1.76 RPM
FIN_HG00378	2.38 RPM
GBR_HG00099	2.44 RPM
GBR_HG00111	2.51 RPM
GBR_HG00114	2.34 RPM
GBR_HG00119	1.82 RPM
GBR_HG00131	2.27 RPM
GBR_HG00133	2.10 RPM
GBR_HG00134	1.86 RPM
GBR_HG00137	1.87 RPM
GBR_HG00142	1.92 RPM
GBR_HG00143	2.46 RPM
TSI_NA20512	1.70 RPM
TSI_NA20513	1.52 RPM
TSI_NA20518	3.14 RPM
TSI_NA20532	2.58 RPM
TSI_NA20538	2.58 RPM
TSI_NA20756	1.77 RPM
TSI_NA20765	2.55 RPM
TSI_NA20771	1.50 RPM
TSI_NA20786	1.86 RPM
TSI_NA20798	2.09 RPM
YRI_NA18870	2.06 RPM
YRI_NA18907	1.11 RPM
YRI_NA18916	2.11 RPM
YRI_NA19093	1.87 RPM
YRI_NA19099	1.28 RPM
YRI_NA19114	0.84 RPM
YRI_NA19118	1.51 RPM
YRI_NA19213	2.18 RPM
YRI_NA19214	1.50 RPM
YRI_NA19223	1.59 RPM

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Indel association:

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