RetrogeneDB ID: retro_btau_1524

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 7:14958506..14958686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGN3
• Ensembl ID: ENSBTAG00000001422
• Aliases: None
• Description: High mobility group nucleosome-binding domain-containing protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q3ZBV4]

Sequence

>retro_btau_1524
ATGCCAAAAAGAAAATCCCCAGAGAATACATAAGGGAAGGATGGATCCAAATTAACTGAATAGGGGCCTACCAGACAGTT
TGCCAGGTTTTCAGCAAAACCTGCTTCTTCAAACCCTGAACCTAAACCAAGAAAAAAAAAATCTGCAAAGAAAGAACCTG
GAACAAAGAGTAATATAGGG

Alignment

ORF - retro_btau_1524 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 59. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKRKSPENTEGKDGSKVTKQEPTRRSARLSAKPAPPKPEPKP-RKTSAKKEPAAKVSKG
          MPKRKSPENT.GKDGSK.T...PTR..AR.SAKPA...PEPKP....SAKKEP..K...G
Retrocopy MPKRKSPENT*GKDGSKLTE*GPTRQFARFSAKPASSNPEPKPXXXXSAKKEPGTKSNIG

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	49.17 RPM
ERP005899_muscle	0.00 RPM	42.34 RPM
SRP017611_brain	0.00 RPM	14.11 RPM
SRP017611_kidney	0.00 RPM	59.92 RPM
SRP017611_liver	0.00 RPM	13.44 RPM
SRP030211_testis	0.00 RPM	36.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1524 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1524 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011031	1 retrocopy	retro_amel_1920,
Bos taurus	ENSBTAG00000001422	2 retrocopies	retro_btau_1524 , retro_btau_1558,
Canis familiaris	ENSCAFG00000002809	1 retrocopy	retro_cfam_1013,
Choloepus hoffmanni	ENSCHOG00000007015	1 retrocopy	retro_chof_2241,
Callithrix jacchus	ENSCJAG00000010800	2 retrocopies	retro_cjac_1626, retro_cjac_819,
Mustela putorius furo	ENSMPUG00000018092	1 retrocopy	retro_mputfur_1164,
Otolemur garnettii	ENSOGAG00000016487	1 retrocopy	retro_ogar_190,
Pongo abelii	ENSPPYG00000016791	1 retrocopy	retro_pabe_421,