RetrogeneDB ID: retro_btau_554

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 14:21891010..21891976(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000027760
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CSF2RA
• Ensembl ID: ENSBTAG00000045948
• Aliases: LOC100336606, CSF2RA
• Description: None

Sequence

>retro_btau_554
CTCCTGGCGACGGTGGTCCTCCTCTCTATGGTGCTTGACTCCGCATGGCTCCTCACCCAGGAGCAGCAGGATCTTCCAAC
CGTGAAGCCAAACGCCGGCCTAAATGTGAAGTTTGACCCACAGACGACGAAGCTGACTTGGGACTGCAGGGAAAACGCTA
GCTCTGGGGAATGTGTGCTGATTCACAAGGAGAAGGGGCTGATTAAGAAAAAGGTCAAAGACAGTGAGTGTCAGTGCACG
TTTCAGGACTATTCTCTCCACGGGGGAGTCACGCTTACCGTTGAAGTACATGTCAACCAGAGACGGCTTTCAGAAATGCT
GGTCTACACTAACCCAGGTAGGGAGGGCACGGCTGCCCAAAACTTCTCCTGTGTTATCTACGACGCGGATTTCATGAACT
GCAGCTGGGCCAAGGGCCGAGCGGCTCCCGACGACGTCCAGTACTTTCTGTACATCCGATCAAAGAAAAGAATCGAGAGG
GAATGTCCTCGTTACCTGAAGGACTCGGGGACCCACGTGGGATGTCACCTCCGAGACCTCTCGGGATTAACGTCGTACAG
TTACTTCCTGGTTAACGGTACCAGCCAAGAAACCGGAATCCAGTTCTTCGACTCGGTTTTGCTGTTAAAGGAAATAGAGC
AGTACAACCCACCTGACAACATCACCGTCCAGTGCAACGAGTCCCACTGCCTCATCAGGTGGGAAAAGCCCAGGACCCGA
CAGCCATGGCCCAACAGGGAGTTCCAGTACCAGCTGGACATCCAGAGACGGCGGGATACCAGCAGCAGTAGAAGTCAACT
GATTGTAGTATTTGGTGACTCCGGTAATAGATACAACTTTCCGAAACCGGGATCCAAAGCGAAACATACTGTGAAGATCA
GGACAGCGGACGCCCGGAAAGCCCACTGGGGAGCCTGGAGCCAGCCCGTTGAGTTCGATTCCTCAAGAGCCACAGGTTAT
TCCCTC

Alignment

ORF - retro_btau_554 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 93.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLATVVLLSMVLDSAWLLTQEQQDLPTVKPNASLNVKFDPQTTKLTWDCRENASSGECVLILGSRARLDP
          LLATVVLLSMVLDSAWLLTQEQQDLPTVKPNA.LNVKFDPQTTKLTWDCRENASSGECVLI......L..
Retrocopy LLATVVLLSMVLDSAWLLTQEQQDLPTVKPNAGLNVKFDPQTTKLTWDCRENASSGECVLIHKEKG-LIK

Parental  EQVKDSECQCTFQDYSLHGGVTLTVEVHVNQRRLSEMLVYTNPGREGTAAQNFSCVIYDADFMNCSWAKG
          ..VKDSECQCTFQDYSLHGGVTLTVEVHVNQRRLSEMLVYTNPGREGTAAQNFSCVIYDADFMNCSWAKG
Retrocopy KKVKDSECQCTFQDYSLHGGVTLTVEVHVNQRRLSEMLVYTNPGREGTAAQNFSCVIYDADFMNCSWAKG

Parental  RAAPDDVQYFLYIRSKKRIERECPRYLKDSGTHVGCHLQDLSGLTSYNYFLVNGTSQETGIQFFDSVLLL
          RAAPDDVQYFLYIRSKKRIERECPRYLKDSGTHVGCHL.DLSGLTSY.YFLVNGTSQETGIQFFDSVLLL
Retrocopy RAAPDDVQYFLYIRSKKRIERECPRYLKDSGTHVGCHLRDLSGLTSYSYFLVNGTSQETGIQFFDSVLLL

Parental  KEIEQYNPPDNITVQCNESHCLIRWEKPRTRQPWPNREFQYQLDIQRRRDTTSGRSQLIVVFGDSGNRYN
          KEIEQYNPPDNITVQCNESHCLIRWEKPRTRQPWPNREFQYQLDIQRRRDT.S.RSQLIVVFGDSGNRYN
Retrocopy KEIEQYNPPDNITVQCNESHCLIRWEKPRTRQPWPNREFQYQLDIQRRRDTSSSRSQLIVVFGDSGNRYN

Parental  FPKPGSKAKHTVKIRTADARKAHWGAWSQPVEF-GSEETGSSL
          FPKPGSKAKHTVKIRTADARKAHWGAWSQPVEF..S..TG.SL
Retrocopy FPKPGSKAKHTVKIRTADARKAHWGAWSQPVEFDSSRATGYSL

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
ERP005899_liver	0.07 RPM	0.94 RPM
ERP005899_muscle	0.69 RPM	4.38 RPM
SRP017611_brain	2.01 RPM	5.25 RPM
SRP017611_kidney	0.59 RPM	2.49 RPM
SRP017611_liver	0.30 RPM	1.28 RPM
SRP030211_testis	0.39 RPM	0.53 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_554 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_554 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_554 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000045948	1 retrocopy	retro_btau_554 ,