RetrogeneDB ID: retro_btau_18

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:91260542..91260908(+)
• Located in intron of: ENSBTAG00000005866

Retrocopy information

• Ensembl ID: ENSBTAG00000017660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: C16H1ORF21
• Ensembl ID: ENSBTAG00000038079
• Aliases: None
• Description: None

Sequence

>retro_btau_18
ATGCGCTGTGCCTCCACCAAGCATGTTGCCACTGTTCAAAACGAAGAGGAAGCCCAGAAAGGGAAGAACTACCAGAATGG
AGATGTGTTTGGCGATGAGTATAGGATCAAACCGGTGGAAGAGGTCAAATACATGAAAAATGGGGCAGAAGAGGAGCAGA
AAATAGCAGCCAGGAACCAAGAAAACTTGGGAAAAAGTGCCAGTTCAAATGTAAGACTTAAAACTAATAAAGAGATTTCA
GGATTAGTTCATCAACCCAGAGCAAACATGCACATTTCTGAAAGCCAACAAGAATTCTTCAGAATGCTGGATGAAAAAAT
TGAAAAGGGTCGAGATTACTGTTCAGAAGAAGAAGGTATCACATAG

Alignment

ORF - retro_btau_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCASAKHVATVQNEEEAQKGKNYQNGDVFGDEYRIKPVEEVKYMKNGAEEEQKIAARNQENLEKSASSN
          M.CAS.KHVATVQNEEEAQKGKNYQNGDVFGDEYRIKPVEEVKYMKNGAEEEQKIAARNQENL.KSASSN
Retrocopy MRCASTKHVATVQNEEEAQKGKNYQNGDVFGDEYRIKPVEEVKYMKNGAEEEQKIAARNQENLGKSASSN

Parental  VRLKTNKEIPGLVHQPRANMHISESQQEFFRMLDEKIEKGRDYCSEEEDIT
          VRLKTNKEI.GLVHQPRANMHISESQQEFFRMLDEKIEKGRDYCSEEE.IT
Retrocopy VRLKTNKEISGLVHQPRANMHISESQQEFFRMLDEKIEKGRDYCSEEEGIT

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	15.64 RPM
ERP005899_muscle	0.05 RPM	7.55 RPM
SRP017611_brain	0.05 RPM	16.22 RPM
SRP017611_kidney	0.18 RPM	15.94 RPM
SRP017611_liver	0.00 RPM	4.91 RPM
SRP030211_testis	0.02 RPM	3.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_18 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_18 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013468	2 retrocopies	retro_amel_508, retro_amel_590,
Bos taurus	ENSBTAG00000038079	3 retrocopies	retro_btau_1219, retro_btau_1661, retro_btau_18 ,
Canis familiaris	ENSCAFG00000013460	1 retrocopy	retro_cfam_1069,
Mustela putorius furo	ENSMPUG00000011816	1 retrocopy	retro_mputfur_1583,
Sorex araneus	ENSSARG00000013999	1 retrocopy	retro_sara_185,