RetrogeneDB ID: retro_ptro_331

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 1:112085656..112087167(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040450
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDIA3
• Ensembl ID: ENSPTRG00000007002
• Aliases: None
• Description: Pan troglodytes protein disulfide isomerase family A, member 3 (PDIA3), mRNA. [Source:RefSeq mRNA;Acc:NM_001246452]

Sequence

>retro_ptro_331
ATGTGCCTCCGCCGCCTAGCGCTGTTCCCGGGCGTGGCGCTGCTTCTCGCCGCGGCCCGCCTCGCGGCTGCCTCCGACGT
GCTAGGACTCAGGGACGACAACTTGGAGAGTCGCATCTCCGACACGGGCTCTGCGGGCCTCATGCTCGTCGAGTTCTTCG
CCCCCTGGTGTGGACACTGCAAGAGACTTGCTCCTGAGTATGAAGCTGCAGCTACCAGATTAAAAGGAATAGTCCCATTA
GCAAAGGCTGATTGCACTGCCAACACTAACACCTGTAATAAATATGGAGTCAGTGGATATCCAACCCTGAAGATATTTAG
AGATGGTGAAGAAGCAGGTGCTTATGATGGACCTAGGACTGCTGATGGAATTGTCAGCCACCTGAAGAAGCAGGCAGGAC
CAGCTTCAGTGCCTCTCAGGACTGAGGAAGAATTTAAGAAATTCATTAGTGATAAAGATGCCTCTATAGTAGGTTTTTTA
GATGATTCATTCAGTGAAGCTCACTCCGAGTTCCTAAAAGCAGCCAGCAACTTGAGGGATAACTACCGATTTGCACATAC
GAATGTTGAGTCTCTGGTGAACGAGTATGATGATAATGGAGATGGTATCATCTTATTTCGTCCTTCACATCTCACTAACA
AGTTGGAGGACAAGACTGTGGCATATACAGAGCAAAAAATGACCAGTGGCAAAATTAAAAAGTTTATCCAGGAAAACATT
TTTGGTATCTGCCCTCACATGACAGAAGACAATAAAGATTTGATACAGGGCAAGGACTTAGTTATTGCTTACTATGATGT
GGACTATGAAAAGAATGCTAAAGGTTCCAACTACTGGAGAAACAGGGTAATGATGGTGGCAAAGAAATTCCTGGATGCTG
GGCACAAACTCAACTTTGCTGTAGCTAGCCGCAAAACCTTTAGCCATGAACTTTCTGATTTTGGCTTGGAGAGCACTGCT
GGAGAGATTCCTGTTGTTGCTATCAGAACTGCTAAAGGAGAGAAGTTTGTCATGCAGGAGGATTTCTCGCATGATGGGAA
TGCTCTGGAGAGGTTCCTGCAGGATTACTTTGATGGCAATCTGAAGAGATACCTGAAGTCTGAACCTATCCCAGAGAGCA
ATGATGGGCCTGTGAAGGTAGTGGTAGCAGAGAATTTTGATGAAATAGTGAATAATGAAAATAAAGATGTGCTGATTGAA
TTTTATGCCCCTTGGTGTGGTCACTGTAAGAACCTGGAGCCCAAGTATAAAGAACTTGGCGAGAAGCTCAGCAAAGACCT
GAATATTGTCATAGCCAAGATGGATGCCACAGCCAATGATGTGCCTTCTCCATATGAAGTCAGAGTTTTCCTACCATATA
CTTCTCTCCAGCCAACAAGAAGCTAAATCCAAAGAAATATGAAGGTGGCCATGAATTAAGTGATTTTATTAGCTATCTAC
AAAGAGAAGCTACAAACCCCCCTGTAATTCAAGAAGAAAAACCCAAGAAGAAGAAGGCACAGGAGGATCTC

Alignment

ORF - retro_ptro_331 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.64 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLRRLALFPGVALLLAAARLAAASDVLELTDDNFESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
          M.LRRLALFPGVALLLAAARLAAASDVL.L.DDN.ESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA
Retrocopy MCLRRLALFPGVALLLAAARLAAASDVLGLRDDNLESRISDTGSAGLMLVEFFAPWCGHCKRLAPEYEAA

Parental  ATRLKGIVPLAKVDCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
          ATRLKGIVPLAK.DCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR
Retrocopy ATRLKGIVPLAKADCTANTNTCNKYGVSGYPTLKIFRDGEEAGAYDGPRTADGIVSHLKKQAGPASVPLR

Parental  TEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGEGIILFRPSH
          TEEEFKKFISDKDASIVGF.DDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNG.GIILFRPSH
Retrocopy TEEEFKKFISDKDASIVGFLDDSFSEAHSEFLKAASNLRDNYRFAHTNVESLVNEYDDNGDGIILFRPSH

Parental  LTNKFEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLLIAYYDVDYEKNAKGSNYWR
          LTNK.EDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDL.IAYYDVDYEKNAKGSNYWR
Retrocopy LTNKLEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLVIAYYDVDYEKNAKGSNYWR

Parental  NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEEFSRDGKALE
          NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQE.FS.DG.ALE
Retrocopy NRVMMVAKKFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTAKGEKFVMQEDFSHDGNALE

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
SRP007412_brain_prefrontal_cortex	1.66 RPM	64.24 RPM
SRP007412_cerebellum	1.33 RPM	57.21 RPM
SRP007412_heart	1.11 RPM	77.85 RPM
SRP007412_kidney	1.62 RPM	181.91 RPM
SRP007412_liver	1.41 RPM	385.87 RPM
SRP007412_testis	0.63 RPM	163.13 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_331 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_331 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_217
Gorilla gorilla	retro_ggor_287

---

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 ,