RetrogeneDB ID: retro_ecab_150

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:139808405..139810515(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000001489
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRKRIR
• Ensembl ID: ENSECAG00000021982
• Aliases: None
• Description: protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor) [Source:HGNC Symbol;Acc:9440]

Sequence

>retro_ecab_150
AAACACTTTGAGACCTCTATGATCTGTCGAAACTAGTCCTTATAGGACAGTTCTTCGAGATAATGCAATACCAACAATAT
TTGATCTTACCAGCCATTTGAACAATCCACATAGTAGACACAGAAAACGAATAAAAGAATTGAGTGAAGATGAAATCAGG
ACACTGAAACAGAAAAAAATTGATGAAACGTCTGAGCAGGAACAGAAACATAAAGAAATAAACAACAGCAGTGCTCAGAA
GCCCAGTGCAGAAGAGGGAGGTGAAGAACAGGATGAAGACATTTTACCTTTAACCCTTGAAGAGAAGGAAAACAAAGAAT
ACTTAAAATCTTTATTTGAAATTTTGATTCTTATGGGAAAACAAAACATACCTCTGGATGGACATGAAGCTGATGAAATC
CCGGAAGGTCTCTTTACTCCTGATAACTTTCAAGCCCTGCTGGAGTGCCGGATAAATTCTGGTGAGGAGGTTCTGAGAAA
GCGCTTTGAGACAACAGCAGTTAACACGTTGTTCTGTTCGAAAACACAGCAGAAGCAGATGTTGGAGATCTGTGAGAGCT
GCATCCGGGAAGAAACCCTCAGGGAGGTGAGAGACTCTCACTTCTTTTCCATTATCACTGACGATGTCGTGGACATAGCA
GGGGAAGAGCACCTGCCTGTGTTGGTGAGGTTTGTTGATGAATCTCATAACCTGAGAGAGGAATTCGTGGGCTTCCTGCC
TTATGAAGCTGATGCAGAAATTTTGGCTGTGAAATTTCACACTACAATAACTGAGAAGTGGGGATTAAACATGGAGTATT
GCCGTGGTCAGGCTTACATTGTGTCCAGTGGATTTTCTTCCAAAATGAAAGTTGTTGCTTCTAGACTTTTAGAGAAATAT
CCCCAAGCCATCTACACACTCTGCTCTTCCTGTGCCTTAAATATGTGGTTGGCAAAATCTGTGCCTGTTATGGGAGTGTC
TGTTGCATTAGGAACAATTGAGGAAGTTTGTTCCTTTTTCCATCGATCACCACAACTGCTTTTAGAACTTGACAATGTAA
TCACTGTCCTCTTTCAGAACAATGAAGAACGGGGTAAAGAACTGAAGGAGATTTGCCATTCTCATTGGACAGGCAGGCAT
GATGCTTTCGAGATTTTAGTGGACCTCCTCCAGGCACTTGTTTTATGTTTAGATGGTATAAATAGTGACACAAGTATTAG
ATAGAATAACTGTATAGCTGGCCGAGCATTTGTCCTCTGTAGTGCAGTAACAGATTTTGATTTCATCGTTACCATTGTTG
TTCTTAAAAATGTTCTATCTTTTACAAGAGCCTTTGGGAAAAATCTCCAGGGGCAAACCTCTGATGTCTTCTTTGCAGCC
AGTAGCTTGACTGCAGTGCTGCATTCACTAAATGAAGTGATGGAAAATATTGAAGTTTATCATGAATTTTGGTTTGAGGA
AGCCACAAATTTGGCAACCAAACTTGATATTCAAATGAAGCTCCCTGGGAAATTCCGCAGAGCACAGCAAGGTAACCTGG
AATCTCAGCTAACCTCTGAGGGTTACTATAAAGAAACTCTGAGTGTCCCAACAGTGGAACACATTATTCAGGAACTGAAA
GATATATTCTCAGAACAGCACCTCAAAGCTCTTAAATGCTTATCTCTGGTCCCGTCTGTCATGGGACAGCTCAAGTTCAA
CACGTCAGAGGAGCATCATGCTGACATGTACAGAAGCGACTTACCCAATCCTGACACGCTCTCGGCCGAGCTGCACTGTT
GGAGAATCAAGTGGAAACACAGAGGGAAAGATATAGAGCTTCCATCCACCATTTATGAAGCCCTCCATCTGCCAGACATC
AAGTTTTTTCCTAATGTTTATGCACTGCTGAAGGTCCTTTGTATCCTTCCTGTGATGAAGGTTGAGAATGAACGCTATGA
AAACGGGCGGAAGCGTCTCAAAGCATACCTGAGGAACACTTTGACAGACCAAAGGTCGAGTAACTTGGCTTTGCTTAACA
TAAATTTTGATATAAAACATGATCTGGATTTAATGGTGGACACATATATCAAACTCTATACAGCTAAGTCGGAGCTTCCT
ACAGAGAATTCAGAAACCATTGAGAATACC

Alignment

ORF - retro_ecab_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.57 %
• Parental protein coverage: 95.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KHFETSMICR-TSPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQK
          KHFETSMICR.TSPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQK
Retrocopy KHFETSMICR>TSPYRTVLRDNAIPTIFDLTSHLNNPHSRHRKRIKELSEDEIRTLKQKKIDETSEQEQK

Parental  HKEINNSSAQKPSAEEGGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHEADEIPEGLFT
          HKEINNSSAQKPSAEEGGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHEADEIPEGLFT
Retrocopy HKEINNSSAQKPSAEEGGEEQDEDILPLTLEEKENKEYLKSLFEILILMGKQNIPLDGHEADEIPEGLFT

Parental  PDNFQALLECRINSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSRFFSIITDDV
          PDNFQALLECRINSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDS.FFSIITDDV
Retrocopy PDNFQALLECRINSGEEVLRKRFETTAVNTLFCSKTQQKQMLEICESCIREETLREVRDSHFFSIITDDV

Parental  VDIAGEEHLPVLVRFVDESHNLREEFVGFLPYEADAEILAVKFHTTITEKWGLNMEYCRGQAYIVSSGFS
          VDIAGEEHLPVLVRFVDESHNLREEFVGFLPYEADAEILAVKFHTTITEKWGLNMEYCRGQAYIVSSGFS
Retrocopy VDIAGEEHLPVLVRFVDESHNLREEFVGFLPYEADAEILAVKFHTTITEKWGLNMEYCRGQAYIVSSGFS

Parental  SKMKVVASRLLEKYPQAIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVITV
          SKMKVVASRLLEKYPQAIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVITV
Retrocopy SKMKVVASRLLEKYPQAIYTLCSSCALNMWLAKSVPVMGVSVALGTIEEVCSFFHRSPQLLLELDNVITV

Parental  LFQNNEERGKELKEICHSHWTGRHDAFEILVDLLQALVLCLDGINSDTSIRWNNCIAGRAFVLCSAVTDF
          LFQNNEERGKELKEICHSHWTGRHDAFEILVDLLQALVLCLDGINSDTSIR.NNCIAGRAFVLCSAVTDF
Retrocopy LFQNNEERGKELKEICHSHWTGRHDAFEILVDLLQALVLCLDGINSDTSIR*NNCIAGRAFVLCSAVTDF

Parental  DFIVTIVVLKNVLSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLD
          DFIVTIVVLKNVLSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLD
Retrocopy DFIVTIVVLKNVLSFTRAFGKNLQGQTSDVFFAASSLTAVLHSLNEVMENIEVYHEFWFEEATNLATKLD

Parental  IQMKLPGKFRRAQQGNLESQLTSEGYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKF
          IQMKLPGKFRRAQQGNLESQLTSEGYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKF
Retrocopy IQMKLPGKFRRAQQGNLESQLTSEGYYKETLSVPTVEHIIQELKDIFSEQHLKALKCLSLVPSVMGQLKF

Parental  NTSEEHHADMYRSDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCIL
          NTSEEHHADMYRSDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCIL
Retrocopy NTSEEHHADMYRSDLPNPDTLSAELHCWRIKWKHRGKDIELPSTIYEALHLPDIKFFPNVYALLKVLCIL

Parental  PVMKVENERYENGRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTAKSELPTENSET
          PVMKVENERYENGRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTAKSELPTENSET
Retrocopy PVMKVENERYENGRKRLKAYLRNTLTDQRSSNLALLNINFDIKHDLDLMVDTYIKLYTAKSELPTENSET

Parental  IENT
          IENT
Retrocopy IENT

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
SRP021940_articular_cartilage	0.00 RPM	3.72 RPM
SRP021940_cerebellum	0.00 RPM	1.61 RPM
SRP021940_embryo	0.33 RPM	6.70 RPM
SRP021940_placental_villous	0.00 RPM	2.41 RPM
SRP021940_synovial_membrane	0.05 RPM	3.16 RPM
SRP021940_testis	0.00 RPM	1.34 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_150 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_150 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_150 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,