RetrogeneDB ID: retro_btau_1601

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:29003258..29003598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAC1
• Ensembl ID: ENSBTAG00000009233
• Aliases: None
• Description: Ras-related C3 botulinum toxin substrate 1 [Source:UniProtKB/Swiss-Prot;Acc:P62998]

Sequence

>retro_btau_1601
ATATTCTCAATTTGCTTTTCCCTTCTGAGTTCTGCATCTTGTGAAAATGTCCATGCAACTTATATCCTGAAATGTGACAT
CATTGTCTCAACACCCCCATCGCACTACTGGGAACTAAACTTGACCTTAGGTAGGATAAAGACATGACTGTGAAACTGAA
GGAGAGGATGACTGCTGTCACGTATCCTTATGGCGTAGCCACGGTTGAGGAGATTTGTGCTATGAAATACCAGGAGTGCT
GGGCTCTGATTCAGTGAGGCAGCTACATGGTGTTTGATGAAGCTCTTACAGAAGTTCTCTCCCACCTCGCAGCAAGAGGA
TGAGAGAACACTTGCTGTTG

Alignment

ORF - retro_btau_1601 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.26 %
• Parental protein coverage: 63.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VFLICFSLVSPASFENVRAKW-YPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAM
          .F.ICFSL.S.AS.ENV.A...YPE..HHC.NTPI.L.GTKLDLR.DKD...KLKE...T..TYP.G.A.
Retrocopy IFSICFSLLSSASCENVHATY<YPEM*HHCLNTPIALLGTKLDLR*DKDMTVKLKE-RMTAVTYPYGVAT

Parental  AKEIGAVKYLECSALTQRGLKTVFDEAIRAVL-CPPPVKKRKRKCLL
          ..EI.A.KY.EC.AL.Q.G...VFDEA...VL..PP..K......LL
Retrocopy VEEICAMKYQECWALIQ*GSYMVFDEALTEVL<LPPRSKRMREHLLL

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	26.10 RPM
ERP005899_muscle	0.00 RPM	201.65 RPM
SRP017611_brain	0.00 RPM	102.09 RPM
SRP017611_kidney	0.00 RPM	107.58 RPM
SRP017611_liver	0.00 RPM	33.98 RPM
SRP030211_testis	0.01 RPM	42.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1601 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1601 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1601 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009233	2 retrocopies	retro_btau_1601 , retro_btau_332,
Canis familiaris	ENSCAFG00000015716	1 retrocopy	retro_cfam_496,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Macaca mulatta	ENSMMUG00000021075	4 retrocopies	retro_mmul_1310, retro_mmul_1964, retro_mmul_2642, retro_mmul_721,
Oryctolagus cuniculus	ENSOCUG00000009956	1 retrocopy	retro_ocun_305,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,