RetrogeneDB ID: retro_ggor_287

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 1:126046425..126047573(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000004670
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PDIA3
• Ensembl ID: ENSGGOG00000023440
• Aliases: None
• Description: None

Sequence

>retro_ggor_287
GATGGAGTTGTCAGCCACCTGAAGAAGCAGTCAGGACCAGCTTCAGTGCCTCTCAGGACTGAGGAAGAATTTAAGAAATT
CATTAGTGATAAAGATGCCTCTATAGTAGGTTTTTTCGATGATTCATTCAGTGAAGCTCACTCCGAGTTCCTAAAAGCAG
CCAGCAACTTGAGGGATAACTACCGATTTGCACATACGAATGTTGAGTCTCTGGTGAACGAGTATGATGATAATGGAGAT
GGTATCATCTTATTTCGTCCTTCACATCTCACTAACAAGTTGGAGGACAAGACTGTGGCATATACAGAGCAAAAAATGAC
CAGTGGCAAAATTAAAAAGTTTATCCAGGAAAACATTTTTGGTATCTGCCCTCACATGACAGAAGACAATAAAGATTTGA
TACAGGGCAAGGACTTACTTATTCTTTACTATGATGTGGACTATGAAAAGAATGCTAAAGGTTCCAACTACTGGAGAAAC
AGGGTAATGATGGTGGCAAAGATATTCCTGGATGCTGGGCACAAACTCAACTTTGCTGTAGCTAGCCGCAAAACCTTTAG
CCATGAACTTTCTGATTTTGGCTTGGAGAGCACTGCTGGAGAGATTCCTGTTGTTGCTATCAGAACTGCTAAAGGAGAGA
AGTTTGTCATGCAGGAGGAGTTCTCATGTGATGGGAATGCTCTGGAGAGATTCCTGCAGGATTACTTTGATGGCAATCTG
AAGAGATACCTGAAGTCTGAACCTATCCCAGAGAGCAATGATGGGCCTGTGAAGGTAGTGGTAGCAGAGAATTTTGATGA
AATAGTGAATAATGAAAATAAAGATGTGCTGATTGAATTTTATGCCCCTTCGTGTGGTCACTGTAAGAACCTGGAGCCCA
AGTATAAAGAACTTGGCGAGAAGCTCAGCAAAGACCTGAATATCGTCATAGCCAAGATGGATGCCACAGCCAATGATGTG
CCTTCTCCATATGAAGTCAGAGTTTTCCTACCATATACTTCTCTCCAGCCAACAAGAAGCTAAATCCAAAGAAATATGAA
GGTGGCCATGAATTAAGTGATTTTATTAGCTATCTACAACGAGAAGCTACAAACCCCCCTGTAATTCAAGAAGAAAAACC
CAAGAAGAAGAAGGCACAGGAGGATCTC

Alignment

ORF - retro_ggor_287 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGIVSHLKKQAGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVES
          DG.VSHLKKQ.GPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVES
Retrocopy DGVVSHLKKQSGPASVPLRTEEEFKKFISDKDASIVGFFDDSFSEAHSEFLKAASNLRDNYRFAHTNVES

Parental  LVNEYDDNGDGIILFGPSHLTNKLEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLL
          LVNEYDDNGDGIILF.PSHLTNKLEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLL
Retrocopy LVNEYDDNGDGIILFRPSHLTNKLEDKTVAYTEQKMTSGKIKKFIQENIFGICPHMTEDNKDLIQGKDLL

Parental  ILYYDVDYEKNAKGSNYWRNRVMMVAKIFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTA
          ILYYDVDYEKNAKGSNYWRNRVMMVAKIFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTA
Retrocopy ILYYDVDYEKNAKGSNYWRNRVMMVAKIFLDAGHKLNFAVASRKTFSHELSDFGLESTAGEIPVVAIRTA

Parental  KGEKFVMQEEFSCDGNALERFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEF
          KGEKFVMQEEFSCDGNALERFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEF
Retrocopy KGEKFVMQEEFSCDGNALERFLQDYFDGNLKRYLKSEPIPESNDGPVKVVVAENFDEIVNNENKDVLIEF

Parental  YAPWCGHCKNLEPKYKELGEKLSKDPNIVIAKMDATANDVPSPYEVR-GFPTIYFSPANKKLNPKKYEGG
          YAP.CGHCKNLEPKYKELGEKLSKD.NIVIAKMDATANDVPSPYEVR..FPTIYFSPANKKLNPKKYEGG
Retrocopy YAPSCGHCKNLEPKYKELGEKLSKDLNIVIAKMDATANDVPSPYEVR<SFPTIYFSPANKKLNPKKYEGG

Parental  RELSDFISYLQREATNPPVIQEEKPKKKKKAQEDL
          .ELSDFISYLQREATNPPVIQEEKP.KKKKAQEDL
Retrocopy HELSDFISYLQREATNPPVIQEEKP-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	5.95 RPM	33.14 RPM
SRP007412_cerebellum	6.34 RPM	28.60 RPM
SRP007412_heart	2.41 RPM	18.61 RPM
SRP007412_kidney	16.81 RPM	120.95 RPM
SRP007412_liver	16.04 RPM	166.60 RPM
SRP007412_testis	30.15 RPM	153.95 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_287 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_287 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_217
Pan troglodytes	retro_ptro_331

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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,