RetrogeneDB ID: retro_cfam_663

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:40028739..40031025(+)
• Located in intron of: ENSCAFG00000006923

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PRKRIR
• Ensembl ID: ENSCAFG00000005274
• Aliases: None
• Description: protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) [Source:HGNC Symbol;Acc:9440]

Sequence

>retro_cfam_663
ATGCCGAACTTCTGCGCTGCCCCCAACTGCACGAGGAAGAGCACGCAGTCAGACCTGGCCTTCTTCAGGTTCCCGCGGGA
TCCGGCCAGATGCCAGAAATGGGTGGAGAATTGTAGGATAGCAGATTTAGAAGATAAAACACCTGATCAACTAAATAAAC
ATTATCGATTATGTGCCAAACACTTTGAGACCTCTATGATCTGTAGAACTAGTCCTTATAGGACAGTTCTTCGTGATAAT
GCAATACCAACAATATTTGATCTTACCAGTCATTTGAACAATCCACATAGTAGACACAGAAAACGAATAAAAGAATTGAG
TGAAGATGAAATCCGGACACTGAAACAGAAAAAAATTGATGAAACTTCTGAACAGGAACCCAAACATAAAGAAATAAACA
ACAGCAATGCTCAGAACCCCAGTGCAGAAGAAGGGGGTGAAGAACAGGATGAAGACATTTTACCTTTGACTCTCGAAGAG
AAAGAAAACAAAGAATACCTAAAATCTTTATTTGAAATTTTGATTCTTATGGGAAAACAAAACATACCTCTGGATGGGCA
TGAAACTGATGAAATCCCAGAGGGTCTCTTTACTCCTGATAACTTTCAAGCACTGCTGGAGTGCCGGATAAATTCTGGTG
AAGAGGTTCTAAGAAAGCGTTTTGAGACAACAGCAGTTAACACATTGTTCTGCTCAAAAACACAACAGAAACAGATGCTA
GAAATCTGTGAGAGCTGCATCCGGGAGGAAACCCTCAGGGAAGTGAGAGACTCTCACTTCTTTTCCATCATCACTGATGA
TGTAGTGGACATAGCAGGGGAAGAACACTTGCCTGTGTTGGTGAGGTTTGTTGATGAATCTCATAACCTGAGAGAGGAAT
TTTTGGGCTTCTTGCCTTACGAAGCCAATGCGGAAATTTTGGCTGTGAAATTTCACACTACAATAATTGAGAAGTGGGGG
TTAAATATGAAATATTGTCGTGGTCAGGCTTACATTGTATCTAGTGGATTTTCTTCCAAAATGAAAATTGTTGCTTCTAG
ACTTTTAGAGAAATATCCCCAAGCTGTCTACACACTTTGTTCTTCCTGTGCCTTAAACATGTGGTTGGCAAAATCAGTGC
CTGTTGTGGGAGTATCTGTTGCATCAGGAACAATCGAGGAAGTTTGTTAGTTCTTCCATCGATCTCCACAACTGCTTTTG
GAGCTTGACAATGTAATTTCTGTCCTCTTTCAGAATAATGAGGAAAAGGGTAAAGAACTGAAGGAAATCTGCCATTCTCA
GTGGACAGGCAGGCATGATGCTTTTGAAATTTTAGTGGATCTCCTACAAGCACTTGTTCTATGTTTAGATGGTATAAATA
GTGATACAAATATTAGATGGAATAACTATATAGCTGGTCGAGCTTTTGTACTCTGTAGTGCAGTAACAGATTTTGATTTC
ATTGTTACCATTGTTGTTCTTAAGAATGTTCTATCTTTTACAAGAGCCTTTGGGAAAAATCTCCAGGGGCAAACCTCTGA
TGTCTTCTTTGCAGCCGGTAGCTTGACTGCAGTGCTGCATTCTCTAAATGAAGTGATGGAAAATATTGAAGTTTATCGTG
AATTTTGGTTCGAAGAAGCCACAAATTTGGCAACTAAACTAGATATTCAGATGAAACTCCCTGGCAAATTCTGCAGAGCG
CAGCAAGGTAACCTGGAATCTCAGCTCACCTCTGAAAGTTACTATAAAGAAACTCTAAGTGTTCCAACAGTGGAACACAT
TATTCAGGAACTGAAAGATATATTCTCAGAACAGCACTTCAAAGCTCTTAAATGCTTATCTCTTGTACCCTCTGTCATGG
AACAGCTCAAATTTAATACATCGGAGGAGCACCATGCTGACATGTACAGAAGTGACCTGCCCAATCCTGACACACTCTCA
GCTGAGCTGCATTGCTGGAGAATCAAGTGGAAACACAGAGGGAAAGATATAGAGCTTCCATCCACCATTTATGAAGCCCT
ACATCTACCAGACATCAAGTTTTATCCTAATTTTTATGCATTGCTCAAAGTCCTATGTATTCTTCCTGTGATGAAGGTTG
AGAATGAACGCTATGAAAATGGGCGAAAGTGTCTCAAAGCATACCTGAGGAACACTTTGACAGACCAAAGGTCAAGTAAC
TTGGCTTTGCTTAACATAAATTTTGATATAAAACGTGATCTGGATTTAATGGTAGACACATATATCAAACTCTATACAAC
TAATTCAGAGCTTCCTACAGATAACTCAGAAACCATTGAAAATACC

Alignment

ORF - retro_cfam_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNFCAAPNCTRKSTQSDLAFFRFPRDPARCQKWVENCRRADLEDKTPDQLNKHYRLCAKHFETSMICRT
          MPNFCAAPNCTRKSTQSDLAFFRFPRDPARCQKWVENCR.ADLEDKTPDQLNKHYRLCAKHFETSMICRT
Retrocopy MPNFCAAPNCTRKSTQSDLAFFRFPRDPARCQKWVENCRIADLEDKTPDQLNKHYRLCAKHFETSMICRT

Parental  SPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEPKHKEINNSNAQNP
          SPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEPKHKEINNSNAQNP
Retrocopy SPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEPKHKEINNSNAQNP

Parental  SAEEGGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHETDEIPEGLFTPDNFQALLECRI
          SAEEGGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHETDEIPEGLFTPDNFQALLECRI
Retrocopy SAEEGGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHETDEIPEGLFTPDNFQALLECRI

Parental  NSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVL
          NSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVL
Retrocopy NSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDVVDIAGEEHLPVL

Parental  VRFVDESHNLREEFLGFLPYEADAEILAVKFHTTITEKWGLNMEYCRGQAYIVSSGFSSKMKIVASRLLE
          VRFVDESHNLREEFLGFLPYEA.AEILAVKFHTTI.EKWGLNM.YCRGQAYIVSSGFSSKMKIVASRLLE
Retrocopy VRFVDESHNLREEFLGFLPYEANAEILAVKFHTTIIEKWGLNMKYCRGQAYIVSSGFSSKMKIVASRLLE

Parental  KYPQAVYTLCSSCALNMWLAKSVPVVGVSVALGTIEEVCSFFHRSPQLLLELDNVISVLFQNNEEKGKEL
          KYPQAVYTLCSSCALNMWLAKSVPVVGVSVA.GTIEEVC.FFHRSPQLLLELDNVISVLFQNNEEKGKEL
Retrocopy KYPQAVYTLCSSCALNMWLAKSVPVVGVSVASGTIEEVC*FFHRSPQLLLELDNVISVLFQNNEEKGKEL

Parental  KEICHSQWTGRHDAFEILVDLLQALVLCLDGINSDTNIRWNNYIAGRAFVLCSAVTDFDFIVTIVVLKNV
          KEICHSQWTGRHDAFEILVDLLQALVLCLDGINSDTNIRWNNYIAGRAFVLCSAVTDFDFIVTIVVLKNV
Retrocopy KEICHSQWTGRHDAFEILVDLLQALVLCLDGINSDTNIRWNNYIAGRAFVLCSAVTDFDFIVTIVVLKNV

Parental  LSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLDIQMKLPGKFRRA
          LSFTRAFGKNLQGQTSDVFFAA.SLTAVLHSLNEVMENIEVY.EFWFEEATNLATKLDIQMKLPGKF.RA
Retrocopy LSFTRAFGKNLQGQTSDVFFAAGSLTAVLHSLNEVMENIEVYREFWFEEATNLATKLDIQMKLPGKFCRA

Parental  QQGNLESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKFNTSEEHHADMYR
          QQGNLESQLTSESYYKETLSVPTVEHIIQELKDIFSEQH.KALKCLSLVPSVM.QLKFNTSEEHHADMYR
Retrocopy QQGNLESQLTSESYYKETLSVPTVEHIIQELKDIFSEQHFKALKCLSLVPSVMEQLKFNTSEEHHADMYR

Parental  SDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCILPVMKVENERYEN
          SDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKF.PN.YALLKVLCILPVMKVENERYEN
Retrocopy SDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFYPNFYALLKVLCILPVMKVENERYEN

Parental  GRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTTKSELPTDNSETIENT
          GRK.LKAYLRNTLTDQRSSNLALLNINFDIK.DLDLMVDTYIKLYTT.SELPTDNSETIENT
Retrocopy GRKCLKAYLRNTLTDQRSSNLALLNINFDIKRDLDLMVDTYIKLYTTNSELPTDNSETIENT

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
SRP012049_cerebellum	0.38 RPM	21.80 RPM
SRP017611_brain	0.08 RPM	14.61 RPM
SRP017611_kidney	0.26 RPM	30.38 RPM
SRP017611_liver	0.15 RPM	10.88 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_663 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_663 has 0 orthologous retrocopies within eutheria group .

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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,