RetrogeneDB ID: retro_btau_905

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 20:30118577..30118878(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSBTAG00000014883
• Aliases: None
• Description: Gamma-aminobutyric acid receptor-associated protein [Source:UniProtKB/Swiss-Prot;Acc:Q9GJW7]

Sequence

>retro_btau_905
TCTGAGAGTGAGACAATACCAAAGAAATACCTGGACCAATTCTGGTGATAGTAGAAAAGGTTCCCAAAGCTCGGATACGA
TACCTGGACAAAAAGAAGTACCTGCTGCCTTCTGATCTTACAGTTGGTCAGTTCTACTTCTTGATCCGGAAATGAATTTG
TCTCTGAGCTGAGAAGGCCTCATTTTTCTTTGCTGTCAGTGTAATTCCACTTGGCAGTGCCCTGATGGGTCATTTATACC
AAGAATATCATGAAAACGCCTGCTTTCTGTACGTTGCCTAGAGTTATGAAGTGTCCACGGT

Alignment

ORF - retro_btau_905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.96 %
• Parental protein coverage: 86.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SEGEKIRKKYPDR-VPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHLRAEDALFFFVNNVI
          SE.E.I.KKY.D....VIVEK.PKARI..LDKKKYL.PSDLTVGQFYFLIRK.I.L.AE.A.FFF...VI
Retrocopy SESETIPKKYLDQ<ILVIVEKVPKARIRYLDKKKYLLPSDLTVGQFYFLIRK*ICL*AEKASFFFAVSVI

Parental  PPTSATMGQLYQEHHEEDFFLYIAYSDE-SVYG
          P..SA.MG.LYQE.HE...FLY.A.S.E.SV.G
Retrocopy PLGSALMGHLYQEYHENACFLYVA*SYE<SVHG

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	195.88 RPM
ERP005899_muscle	0.00 RPM	227.84 RPM
SRP017611_brain	0.00 RPM	121.87 RPM
SRP017611_kidney	0.00 RPM	245.03 RPM
SRP017611_liver	0.00 RPM	150.79 RPM
SRP030211_testis	0.02 RPM	251.51 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_905 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_905 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_905 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011632	1 retrocopy	retro_btau_977,
Bos taurus	ENSBTAG00000014883	1 retrocopy	retro_btau_905 ,
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Dipodomys ordii	ENSDORG00000005229	1 retrocopy	retro_dord_308,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,