RetrogeneDB ID: retro_hsap_4080

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 8:79672379..79674649(-)
• Located in intron of: ENSG00000104432

Retrocopy information

• Ensembl ID: ENSG00000253919
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKRIR
• Ensembl ID: ENSG00000137492
• Aliases: PRKRIR, DAP4, P52rIPK, THAP0, THAP12
• Description: protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) [Source:HGNC Symbol;Acc:9440]

Sequence

>retro_hsap_4080
TGCCGCCAACTGCACGCGGAAGAGCACGCAGTCCGACTTGACTTGGCCTTCTTCAGCTTCCCGCGGGACCCTGCCAGATG
CCAGAAGTGGGTGGAGAACTGTAGGAGAGCAGACTTAGAAGATAAAACACCTGATCAGCTAAATAAACATTATCGATTAT
GTGCCAAACATTTTGAGACCTCTATGATCTGTAGAACTGGTCCTTATAGGACAGTTCTTCGAGATAATGCAATACCAACA
ATATTTGATCTTAACAGTCATTTGAACAACCCACATAGTAGACACAGAAAACGAATAAAAGAACTGAGTGAAGATGAAAT
CAGGACACTGAAACAGAAAAAAATTGATGAAACTTCTGAGCAGGAACAAAAACATAAAGAAACCAACAATAGCAATGCTC
AGAACCCCAGCGAAGAAGAGGGTGAAGGGCAAGATGAGGACATTTTACCTCTAACCCTTGAAGAGAAGGAAAACAAAGAA
TACCTCAAATATCTACTTGAAATCTTGATTCTGATGGGAAGGCAAAACATACCTCTGGACGGACATGAGGCTGATGAAAT
CCCAGAAGGTCTCTTTACTCCAGATAACTTTCAGGCACTACTGGAGTGTCGGATAAATTCTGGTGAAGAGGTTCTGAGAA
AGCGGTTTGAGACAACAGCAGTTAACACGTTGTTTTGTTCAAAAACACAGCAGAGGCAGATGCTAGAGATCTGTGAGAGC
TGTATTCGAGAAGAAACTCTCAGGGAAGTGAGAGACTCACACGTCTTTTCCATTATCACTGACGATGTAGTGGACATAGC
AGGGGAAGAGCACCTACCTGTGTTGGTGAGGTTTGTTGATGAATCTCATAACCTAAGAGAGGAATTTATAGGCTTCCTGC
CTTATGAAGCTGATGCAGAAATTTTGGCTGTGAAATTTCACACTATGATAACTGAGAAGTGGGGATTAAATATGGAGTAT
TGTCGTGGCCAGGCTTACATTGTCTCTAGTGGATTTTCTTCCAAAATGAAAGTTGTTGCTTCTAGACTTTTAGAGAAATA
TCCCCAAGCTATCTACACACTCTGCTCTTTCTGTGCCTTAAATATGTGGTTGGCAAAATCAGTACCTGTTATGGGAGTAT
CTGTTGCATTAGGAACAATCGAGGAAGTTTGTTCTTTTTTCCATCGATCACCACAACTGCTTTTAGAACTTGACAACGTA
ATTTCTGTTCTTTTTCAGAACAGTAAAGAAAGGGGTAAAGAACTGAAGGAAATCTGCCATTCTCAGTGGACAGGGAGGCA
TGATGCTTTTGAAATTTTAGTGGAACTCCTGCAAGCACTTGTTTTATGTTTAGATGGTATAAATAGTGACACAAATATTA
GATGGAATAACTGTATAGCTGGCCGAGCATTTGTACTCTGCAGTGCAGTAACAGATTTTGATTTCATTGTTACTATTGTT
GTTCTTAAAAATGTCCTATCTTTTACAAGAGCCTTTGGGAAAAACCTCCAGGGGCAAACCTCTGATGTCTTCTTTGCAGC
CGGTAGCTTGACTGCAGTACTGCATTCACTCAACGAAGTGATGGAAAATATTGAAGTTTATAATGAATTTTGGTTTGAGG
AAGCCACAAATTTGGCAACCAAACTTGATATTCAAATGAAACTCCCTGGGAAATTCCGCAGAGCTCACCAGGGTAACTTG
GAATCTCAGCTAACCTTTGAGAGTTACTATAAAGAAACCCTAAGTGTCCCAACAGTGGAGCACATTATTCAGGAACTTAA
AGATATATTCTCAGAACAGCACCTCAAAGCTCTTAAATGCTTATCTCTGGTACCCTCAGTCATGGGACAACTCAAATTCA
ATACTTTGGAGGAACACCATGCTGACATGTATAGAAGTGACTTACCCAATCCTGACACGCTGTCAGCTGAGCTTCATTGT
TGGGGAATCAAATGGAAACACAGGGGGAAAGATATAGAGCTTCCGTCCACCATCTATGAAGCCCTCCAACTGCCTGACAT
CAAGTTTTTTCCTAATGTGTATGCATTGCTGAAGGTCCTGTGTATTCTTCTGTGATGAAGGTTGAGAATGAGCGGTATGA
AAATGGATGAAAGCGTCTTAAAGCATATTTGAGGAACACTTTGACAGACCAAAGGTCAAGTAACTTGGCTTTGCTTAACA
TAAATTTTGATATAAAACACGACCTGGATTTAATGGTGGACACATATATTAAACTCTATACAAGTAAGTCAGAGCTTCCT
ACAGATAATTCCGAAACTGTGGAAAATACC

Alignment

ORF - retro_hsap_4080 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.04 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CAAPNCTRKSTQSDLAFFRFPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRTSPYR
          C............DLAFF.FPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRT.PYR
Retrocopy CRQLHAEEHAVRLDLAFFSFPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRTGPYR

Parental  TVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEE
          TVLRDNAIPTIFDL.SHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEE
Retrocopy TVLRDNAIPTIFDLNSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQKHKETNNSNAQNPSEEE

Parental  GEGQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEE
          GEGQDEDILPLTLEEKENKEYLK.L.EILILMG.QNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEE
Retrocopy GEGQDEDILPLTLEEKENKEYLKYLLEILILMGRQNIPLDGHEADEIPEGLFTPDNFQALLECRINSGEE

Parental  VLRKRFETTAVNTLFCSKTQQRQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVLVRFVD
          VLRKRFETTAVNTLFCSKTQQRQMLEICESCIREETLREVRDSH.FSIITDDVVDIAGEEHLPVLVRFVD
Retrocopy VLRKRFETTAVNTLFCSKTQQRQMLEICESCIREETLREVRDSHVFSIITDDVVDIAGEEHLPVLVRFVD

Parental  ESHNLREEFIGFLPYEADAEILAVKFHTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQA
          ESHNLREEFIGFLPYEADAEILAVKFHTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQA
Retrocopy ESHNLREEFIGFLPYEADAEILAVKFHTMITEKWGLNMEYCRGQAYIVSSGFSSKMKVVASRLLEKYPQA

Parental  IYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICH
          IYTLCS.CALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICH
Retrocopy IYTLCSFCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNSKERGKELKEICH

Parental  SQWTGRHDAFEILVELLQALVLCLDGINSDTNIRWNNYIAGRAFVLCSAVSDFDFIVTIVVLKNVLSFTR
          SQWTGRHDAFEILVELLQALVLCLDGINSDTNIRWNN.IAGRAFVLCSAV.DFDFIVTIVVLKNVLSFTR
Retrocopy SQWTGRHDAFEILVELLQALVLCLDGINSDTNIRWNNCIAGRAFVLCSAVTDFDFIVTIVVLKNVLSFTR

Parental  AFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRAHQGNL
          AFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVY.EFWFEEATNLATKLDIQMKLPGKFRRAHQGNL
Retrocopy AFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVYNEFWFEEATNLATKLDIQMKLPGKFRRAHQGNL

Parental  ESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTSEEHHADMYRSDLPN
          ESQLT.ESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNT.EEHHADMYRSDLPN
Retrocopy ESQLTFESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTLEEHHADMYRSDLPN

Parental  PDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCIL-PVMKVENERYENGRKR
          PDTLSAELHCW.IKWKHRGKDIELPSTIYEAL.LPDIKFFPNVYALLKVLCIL..VMKVENERYENG.KR
Retrocopy PDTLSAELHCWGIKWKHRGKDIELPSTIYEALQLPDIKFFPNVYALLKVLCIL<SVMKVENERYENG*KR

Parental  LKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETVENT
          LKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETVENT
Retrocopy LKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTSKSELPTDNSETVENT

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	0.18 RPM	37.15 RPM
bodymap2_adrenal	0.31 RPM	51.36 RPM
bodymap2_brain	0.12 RPM	27.00 RPM
bodymap2_breast	0.12 RPM	48.33 RPM
bodymap2_colon	0.15 RPM	32.23 RPM
bodymap2_heart	0.17 RPM	22.21 RPM
bodymap2_kidney	0.43 RPM	36.60 RPM
bodymap2_liver	0.00 RPM	13.52 RPM
bodymap2_lung	0.19 RPM	31.08 RPM
bodymap2_lymph_node	0.09 RPM	39.25 RPM
bodymap2_ovary	0.19 RPM	66.87 RPM
bodymap2_prostate	0.19 RPM	37.50 RPM
bodymap2_skeletal_muscle	0.02 RPM	19.81 RPM
bodymap2_testis	0.28 RPM	46.15 RPM
bodymap2_thyroid	0.26 RPM	49.87 RPM
bodymap2_white_blood_cells	0.85 RPM	102.32 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4080 was not detected

EST

1 EST(s) were mapped to retro_hsap_4080 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA362001	79672855	79673141	97.9	278	3	273

TSS

No TSS is located nearby retro_hsap_4080 retrocopy 5' end.

Lab

retro_hsap_4080 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4080 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2766

---

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,