RetrogeneDB ID: retro_btau_261

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 1:72626672..72626938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000034519
• Aliases: None
• Description: None

Sequence

>retro_btau_261
CTGCCCCTCCTACCCTAAGTCAGTAGTGACTCCCTGGAGGCTTACGTGTGGGCGCCTTTCTTCCTCACCCTGGTTGAGGT
GGTAGGGGCTGTGGTAATATATTTCCAGGAGAAAAAGCAGGTGGACTGGCTTCATCGTCACTGCCACCCCTGTGCAGCTA
CAGCCCTGTTGAGATACACGAGGCTGAACAGGGGCTCTTCTCTGACGTGGGGGACCCCAAGGTGGTACATGCCTGGCAAA
GTGGCTACCAGCTCAAGCGAATGCCT

Alignment

ORF - retro_btau_261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.04 %
• Parental protein coverage: 89.22 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VPNAPQANSDSMVGYVLGPFFLITLVGVVVAVVMYIQKRKRVDRLRHH-LLPMYSYDPAEELHEAEQELL
          .P..P...SDS...YV..PFFL.TLV.VV.AVV.Y.Q..K.VD.L..H.L.P..SY.P.E..HEAEQ.L.
Retrocopy LPLLP*VSSDSLEAYVWAPFFL-TLVEVVGAVVIYFQEKKQVDWLHRH<LPPLCSYSPVE-IHEAEQGLF

Parental  SDVGDPKVVHGWQSGYQHKRMP
          SDVGDPKVVH.WQSGYQ.KRMP
Retrocopy SDVGDPKVVHAWQSGYQLKRMP

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	0.87 RPM
ERP005899_muscle	0.00 RPM	6.65 RPM
SRP017611_brain	0.00 RPM	11.51 RPM
SRP017611_kidney	0.00 RPM	3.67 RPM
SRP017611_liver	0.00 RPM	1.36 RPM
SRP030211_testis	0.01 RPM	6.59 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_261 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_261 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_474

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001058	1 retrocopy	retro_amel_1014,
Bos taurus	ENSBTAG00000034519	1 retrocopy	retro_btau_261 ,
Equus caballus	ENSECAG00000005108	3 retrocopies	retro_ecab_236, retro_ecab_474, retro_ecab_700,
Myotis lucifugus	ENSMLUG00000011876	1 retrocopy	retro_mluc_137,
Mus musculus	ENSMUSG00000062753	1 retrocopy	retro_mmus_1543,
Oryctolagus cuniculus	ENSOCUG00000013398	1 retrocopy	retro_ocun_625,
Pelodiscus sinensis	ENSPSIG00000004692	1 retrocopy	retro_psin_32,