RetrogeneDB ID: retro_btau_1193

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:22354272..22354653(-)
• Located in intron of: ENSBTAG00000021654

Retrocopy information

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

Parental gene information

• Parental gene symbol: CGI-119
• Ensembl ID: ENSBTAG00000026993
• Aliases: TMBIM4, CGI-119
• Description: transmembrane BAX inhibitor motif-containing protein 4 [Source:RefSeq peptide;Acc:NP_001014914]

Sequence

>retro_btau_1193
TTTTTTAATACCAGATGGACCTTTGTACATGAAAGTCTGGCCTTAATTTTGGTGTTTTCTCTTGGATCTTTTGGTCTGAT
TTCAGCCATGACTTTAAACAGACATAAGCATCCCCTTAGCCCATCCCTGCTCTTTGTATTTATAGTGTTGGAAGCTCTGA
CTGTGGCCTTCATTGTTACTTTCTGTGATGTACATATTGTCCTGCAAGATTGTATACTGACCCATGCAGTATTTCCTGAT
TCAACTGTGTATACTCTGCAGTCTAAGAGAGACTGCAGCAAATTTGGAGCAGGCCTATTTTCTGGTTTGTGGATTTTGTT
CTTGTCAGGAATCTTGAAGGTGTTTTGTTATGGTGAAACAGTGGAGCTGGTCGTGGCTTCT

Alignment

ORF - retro_btau_1193 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 53.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YFDSIRTFVHESPALILVLALGSLGLILALTVNRHKHPLNLYLLFGFTLLESLTVAFVVTFYDVYVVLQA
          .F....TFVHES.ALILV..LGS.GLI.A.T.NRHKHPL...LLF.F..LE.LTVAF.VTF.DV..VLQ.
Retrocopy FFNTRWTFVHESLALILVFSLGSFGLISAMTLNRHKHPLSPSLLFVFIVLEALTVAFIVTFCDVHIVLQD

Parental  FILTCAVFLGLTVYTLQSKRDFSKFGAGLFAGLWILCLSGILRLFFYSETVELVLAA
          .ILT.AVF...TVYTLQSKRD.SKFGAGLF.GLWIL.LSGIL..F.Y.ETVELV.A.
Retrocopy CILTHAVFPDSTVYTLQSKRDCSKFGAGLFSGLWILFLSGILKVFCYGETVELVVAS

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	191.20 RPM
ERP005899_muscle	0.00 RPM	99.98 RPM
SRP017611_brain	0.00 RPM	71.31 RPM
SRP017611_kidney	0.00 RPM	168.39 RPM
SRP017611_liver	0.00 RPM	114.92 RPM
SRP030211_testis	0.00 RPM	224.04 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1193 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1193 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1193 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026993	1 retrocopy	retro_btau_1193 ,
Tarsius syrichta	ENSTSYG00000010967	3 retrocopies	retro_tsyr_1322, retro_tsyr_1408, retro_tsyr_936,