RetrogeneDB ID: retro_ptro_2766

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:76801875..76804068(-)
• Located in intron of: ENSPTRG00000020362

Retrocopy information

• Ensembl ID: ENSPTRG00000034039
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKRIR
• Ensembl ID: ENSPTRG00000004091
• Aliases: None
• Description: Protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) [Source:UniProtKB/TrEMBL;Acc:K7DMS0]

Sequence

>retro_ptro_2766
TGCCAGAAGTGGGTGGAGAACTGTAGGAAAGCAGACTTAGAAGATAAAACACCTGATCAGCTAAATAAACATTATCGATT
ATGTGCCAAACATTTTGAGACCTCTATGATCTGTAGAACTAGTCCTTATAGGACAGTTCTTCGAGATAATGCAATACCAA
CAATATTTGATCTTACCAGTCATTTGAACAACCCACATAGTAGACACAGAAAACGAATAAAAGAACTGAGTGAAGATGAA
ATCAGGACACTGAAACAGAAAAAAATTGATGAAACTTCTGAGCAGGAACAAAAACACAAAGAAACCAACAATAGCAATGC
TCAGAACCCCAGCGAAGAAGAGGGTGAAGGGCAAGATGAGGACATTTTACCTCTAACCCTTGAAGAGAAGGAAAACAAAG
AATACCTAAAATATCTATTTGAAATCTTGATTCTGATGGGAAGGCAAAACATACCTCTGGACGGACATGAGGCTGATGAA
ATCGCAGAAGGTCTCTTTACTCCAGATAACTTTCAGGCACTGCTGGAGTGTCGGATAAATTCTGGTGAAGAGGTTCTGAG
AAAGCGGTTTGAGACAACAGCAGTTAACACGTTGTTTTGTTCAAAAACACAGCAGAGGCAGATGCTAGAGATCTGTGAGA
ACTGTATTCGAGAAGAAACTCTCAGGGAAGTGAGAGACTCACACGTCTTTTCCATTATCACTGACGATGTAGTGGACATA
GCAGGGGAAGAGCACCTACCTGTGTTGGTGAGGTTTGTTGATGAATCTCATAACCTAAGAGAGGAATTTATAGGCTTCCT
GCCTTATGAAGCTGATGCAGAAATTTTGGCTGTGAAATTTCACACTATGATAACTGAGAAGTGGGGATTAAATATGGAGT
ATTGTCGTGGCCAGGCTTACATTGTCTCTAGTGGATTTTCTTCCAAAATGAAAGTTGTTGCTTCTAGACTTTTAGAGAAA
TATCCCCAAGCTATCTACACACTCTGCTCTTTCTGTGCCTTAAATATGTGGTTGGCAAAATCAGTACCTGTTATGGGAGT
ATCTGTTGCATTAGGAACAATCGAAGAAGTTTGTTCTTTTTTCCATCGATCACCACAACTGCTTTTAGAACCTGACAACG
TAATTTCTGTTCTTTTTCAGAACAGTAAAGAAAGGGGTAAAGAACTGAAGGAAATCTGCCATTCTCAGTGGACAGGCAGG
CATGATGCTTTTGAAATTTTAGTGGAACTCCTGCAAGCACTTGTTTTATGTTTAGATGGTATAAATAGTGACACAAATAT
TAGATGGAATAACTATATAGCTGGCCGAGCATTTGTACTCTGCAGTGCAGTAACAGATTTTGATTTCATTGTTACTATTG
TTGTTCTTAAAAACGTCCTATCTTTTACAAGAGCCTTTGGGAAAAACCTCCAGGGGCAAACCTCTGATGTCTTCTTTGCA
GCCGGTAGCTTGACTGCAGTACTGCATTCACTCAACGAAGTGATGGAAAACATTGAAGTTTATAATGAATTTTGGTTTGA
GGAAGCCACAAATTTGGCAACCAAACTTGATATTCAAATGAAACTCCCTGGGAAATTCCGCAGAGCTCACCAGGGTAACT
TGGAATCTCAGCTAACCTCTGAGAGTTACTATAAAGAAACCCTAAGTGTCCCAACAGTGGAGCACATTATTCAGGAACTT
AAAGATATATTCGCAGAACAGCACCTCAAAGCTCTTAAATGCTTATCTCTGGTACCCTCAGTCATGGGACAACTCAAATT
CAATACGTCGGATGGAACACCATGCTGACATGTATAGAAGTGACTTACCCAATCCTGACACGCTGTCAGCTGAGCTTCAT
TGTTGGGGAATCAAATGGAAACACAGGGGGAAAGATATAGAGCTTCCGTCCACCATCTATGAAGCCCTCCAACTGCCTGA
CATCAAGTTTTTTCCTAATGTGTATGCATTGCTGAAGGTCCTGTGTATTCTTCTGTGATGAAGGTTGAGAATGAGCGGTA
TGAAAATGGACGAAAGCGTCTTAAAGCATATTTGAGGAACACTTTGACAGACCAAAGGTCAAGTAACTTGGCTTTGCTTA
ACATAAATTTTGATATAAAACACGACCTGGATTTAATGGTGGACACATATATTAAACTCTATACAAGTAAGTCAGAGCTT
CCTACAGATAATTCCGAAACTGTGGAAAATACC

Alignment

ORF - retro_ptro_2766 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRTSPYRTVLRDNAIPTIFDLTSHLNNPHSRHR
          CQKWVENCR.ADLEDKTPDQLNKHYRLCAKHFETSMICRTSPYRTVLRDNAIPTIFDLTSHLNNPHSRHR
Retrocopy CQKWVENCRKADLEDKTPDQLNKHYRLCAKHFETSMICRTSPYRTVLRDNAIPTIFDLTSHLNNPHSRHR

Parental  KRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEEGEGQDEDILPLTLEEKENKEYLKSLF
          KRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEEGEGQDEDILPLTLEEKENKEYLK.LF
Retrocopy KRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEEGEGQDEDILPLTLEEKENKEYLKYLF

Parental  EILILMGKQNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEEVLRKRFETTAVNTLFCSKTQQRQMLE
          EILILMG.QNIPLDGHEADEI.EGLFTPDNFQALLECRINSGEEVLRKRFETTAVNTLFCSKTQQRQMLE
Retrocopy EILILMGRQNIPLDGHEADEIAEGLFTPDNFQALLECRINSGEEVLRKRFETTAVNTLFCSKTQQRQMLE

Parental  ICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVLVRFVDESHNLREEFIGFLPYEADAEILAVKF
          ICE.CIREETLREVRDSH.FSIITDDVVDIAGEEHLPVLVRFVDESHNLREEFIGFLPYEADAEILAVKF
Retrocopy ICENCIREETLREVRDSHVFSIITDDVVDIAGEEHLPVLVRFVDESHNLREEFIGFLPYEADAEILAVKF

Parental  HTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQAIYTLCSSCALNMWLAKSVPVMGVSVA
          HTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQAIYTLCS.CALNMWLAKSVPVMGVSVA
Retrocopy HTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQAIYTLCSFCALNMWLAKSVPVMGVSVA

Parental  LGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICHSQWTGRHDAFEILVELLQALVLCLDG
          LGTIEEVCSFFHRSPQLLLE.DNVISVLFQNSKERGKELKEICHSQWTGRHDAFEILVELLQALVLCLDG
Retrocopy LGTIEEVCSFFHRSPQLLLEPDNVISVLFQNSKERGKELKEICHSQWTGRHDAFEILVELLQALVLCLDG

Parental  INSDTNIRWNNYIAGRAFVLCSAVSDFDFIVTIVVLKNVLSFTRAFGKNLQGQTSDVFFAAGSLTAVLHS
          INSDTNIRWNNYIAGRAFVLCSAV.DFDFIVTIVVLKNVLSFTRAFGKNLQGQTSDVFFAAGSLTAVLHS
Retrocopy INSDTNIRWNNYIAGRAFVLCSAVTDFDFIVTIVVLKNVLSFTRAFGKNLQGQTSDVFFAAGSLTAVLHS

Parental  LNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRAHQGNLESQLTSESYYKETLSVPTVEHIIQEL
          LNEVMENIEVY.EFWFEEATNLATKLDIQMKLPGKFRRAHQGNLESQLTSESYYKETLSVPTVEHIIQEL
Retrocopy LNEVMENIEVYNEFWFEEATNLATKLDIQMKLPGKFRRAHQGNLESQLTSESYYKETLSVPTVEHIIQEL

Parental  KDIFSEQHLKALKCLSLVPSVMGQLKFNTSE-EHHADMYRSDLPNPDTLSAELHCWRIKWKHRGKDIELP
          KDIF.EQHLKALKCLSLVPSVMGQLKFNTS..EHHADMYRSDLPNPDTLSAELHCW.IKWKHRGKDIELP
Retrocopy KDIFAEQHLKALKCLSLVPSVMGQLKFNTSD>EHHADMYRSDLPNPDTLSAELHCWGIKWKHRGKDIELP

Parental  STIYEALHLPDIKFFPNVYALLKVLCIL-PVMKVENERYENGRKRLKAYLRNTLTDQRSSNLALLNINFD
          STIYEAL.LPDIKFFPNVYALLKVLCIL..VMKVENERYENGRKRLKAYLRNTLTDQRSSNLALLNINFD
Retrocopy STIYEALQLPDIKFFPNVYALLKVLCIL<SVMKVENERYENGRKRLKAYLRNTLTDQRSSNLALLNINFD

Parental  IKHDLDLMVDTYIKLYTSKSELPTDNSETVENT
          IKHDLDLMVDTYIKLYTSKSELPTDNSETVENT
Retrocopy IKHDLDLMVDTYIKLYTSKSELPTDNSETVENT

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	0.43 RPM	12.32 RPM
SRP007412_cerebellum	0.50 RPM	10.43 RPM
SRP007412_heart	0.44 RPM	9.04 RPM
SRP007412_kidney	0.42 RPM	9.94 RPM
SRP007412_liver	0.33 RPM	5.86 RPM
SRP007412_testis	0.32 RPM	12.65 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2766 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2766 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4080

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000024488	1 retrocopy	retro_acar_167,
Bos taurus	ENSBTAG00000031609	2 retrocopies	retro_btau_1797, retro_btau_780,
Canis familiaris	ENSCAFG00000005274	1 retrocopy	retro_cfam_663,
Equus caballus	ENSECAG00000021982	1 retrocopy	retro_ecab_150,
Homo sapiens	ENSG00000137492	1 retrocopy	retro_hsap_4080,
Mustela putorius furo	ENSMPUG00000008784	1 retrocopy	retro_mputfur_1571,
Pan troglodytes	ENSPTRG00000004091	1 retrocopy	retro_ptro_2766 ,
Tursiops truncatus	ENSTTRG00000013287	1 retrocopy	retro_ttru_126,