RetrogeneDB ID: retro_btau_1181

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:33609974..33610364(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.87276
• Ensembl ID: ENSBTAG00000016472
• Aliases: None
• Description: None

Sequence

>retro_btau_1181
GGGGAGACAGAGGGGGAGAAGGTACTGGGCATGTGTTGGAGAACCAGGTTATGGACGTCTGTATGTACGCCGCCGTCAGG
ATCTGCTACAGATCCGACTTTGAGCAACTGGAGCCCGGTTACTCGAAGGAGATCCCTGAGAAGGTGAGGTTCTTCTCAGA
CTTTCTGGGGAAGAGGCCTTGGCTTGCAGGGGCCAAGCTCACCTAGCTGGACTCCCTGGATTATGACATCCTTGATGGGC
ACCGCCATGTTTGAGCCCAAGTGCCTGGATGAATCCCAAACCTGGAAGACTGCCTTTCCCATGTTGAGGGCCTGAGGATC
TCTGCCCCTGAAGCCCAGTCGCTTCTGCCCAGGGCCTCTGTTTCTGGAGACTGCCCTGTGGGGCAATAGG

Alignment

ORF - retro_btau_1181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.82 %
• Parental protein coverage: 60.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GETEEEMI-RVDILENQVMDV-RFAMARICYSPDFEKLKPGFLKEIPEKIKLFSEFLGKRPWFAGDKLSY
          GETE.E.......LENQVMDV...A..RICY..DFE.L.PG..KEIPEK...FS.FLGKRPW.AG.KL..
Retrocopy GETEGEKV<TGHVLENQVMDVCMYAAVRICYRSDFEQLEPGYSKEIPEKVRFFSDFLGKRPWLAGAKLT*

Parental  VDFLVYDVLDMHR-IFEPKCLDA-FPNLKDFISRFEGLKKISAYMKSSRFLP-GPLFLKLAVWGNK
          .D.L.YD.LD.HR..FEPKCLD...PNL.D..S..EGL..ISA.......LP.GPLFL..A.WGN.
Retrocopy LDSLDYDILDGHR>MFEPKCLDE<IPNLEDCLSHVEGL-RISA-PEAQSLLP>GPLFLETALWGNR

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	0.22 RPM	66.33 RPM
ERP005899_muscle	0.00 RPM	12.72 RPM
SRP017611_brain	0.64 RPM	16.54 RPM
SRP017611_kidney	0.06 RPM	9.25 RPM
SRP017611_liver	0.15 RPM	9.67 RPM
SRP030211_testis	0.04 RPM	4.70 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1181 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1181 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1181 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004970	1 retrocopy	retro_amel_1548,
Bos taurus	ENSBTAG00000016472	1 retrocopy	retro_btau_1181 ,
Canis familiaris	ENSCAFG00000019812	2 retrocopies	retro_cfam_1766, retro_cfam_2062,
Equus caballus	ENSECAG00000024971	1 retrocopy	retro_ecab_1058,
Macaca mulatta	ENSMMUG00000019630	2 retrocopies	retro_mmul_1432, retro_mmul_1806,
Mustela putorius furo	ENSMPUG00000003658	1 retrocopy	retro_mputfur_758,
Mus musculus	ENSMUSG00000027890	1 retrocopy	retro_mmus_204,
Pteropus vampyrus	ENSPVAG00000009559	1 retrocopy	retro_pvam_1047,
Tarsius syrichta	ENSTSYG00000007276	1 retrocopy	retro_tsyr_793,