RetrogeneDB ID: retro_btau_1219

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:34438480..34438699(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000031655
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_btau_1219
ATGGGCTGTGCCTCTGCCAAGCATGTTGCCACTGTTCAAAATGAAGAGGAAGCCCAGAAAGGGAAGAACTACCAGAACGG
AGATGTGTTTCGCGATGAGTATAGGATCAAACCGGTGGAAGAGGTCAAATACATGAAAAACGGGGCAGAAGAGGAGCAGA
AGATAGCAGTCAGGAACCAAGAAACCTTGGAAAAAAGTGAGAGTTCAAATGTAAGACTT

Alignment

ORF - retro_btau_1219 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.52 %
• Parental protein coverage: 60.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGCASAKHVATVQNEEEAQKGKNYQNGDVFGDEYRIKPVEEVKYMKNGAEEEQKIAARNQENLEKSASSN
          MGCASAKHVATVQNEEEAQKGKNYQNGDVF.DEYRIKPVEEVKYMKNGAEEEQKIA.RNQE.LEKS.SSN
Retrocopy MGCASAKHVATVQNEEEAQKGKNYQNGDVFRDEYRIKPVEEVKYMKNGAEEEQKIAVRNQETLEKSESSN

Parental  VRL
          VRL
Retrocopy VRL

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	0.00 RPM	15.64 RPM
ERP005899_muscle	0.00 RPM	7.55 RPM
SRP017611_brain	0.00 RPM	16.22 RPM
SRP017611_kidney	0.06 RPM	15.94 RPM
SRP017611_liver	0.00 RPM	4.91 RPM
SRP030211_testis	0.01 RPM	3.02 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1219 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1219 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1219 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,