RetrogeneDB ID: retro_btau_458

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:9339869..9340475(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000039720
• Aliases: None
• Description: transmembrane protein 225-like [Source:RefSeq peptide;Acc:NP_001091490]

Sequence

>retro_btau_458
GTAGCCTCCCTGGGCTACCTGCTTATCCTGCTGGTCTCCATCTTCCCCTTCTGGGTGCGGCTGGTGAACGAGGAGTCCCA
GGAAGTGTTCTTCAGTGGCCTGTTTGAGAACTGCTTCCATATCAAGTGCTGGAAGCCTCGACCCTTATCCATTTACGTCA
TCCTCGGCCGAGTCTCCCTGCTGTCCGCCGTTGTCTTGTCTTTCCTCACCACTTTCATCATGGTGTCCTTTGCGTCTCAG
CTCTTTCCGAGGACCCGGAAGCACAATTTTGTGTCAGCCTTCATCAGTTTCCTCACAGGGGCTTGTGCCTTCCTGGCCTT
GTTGCTGCATGCCCTGGAGATCCAGAGTCTGCGGATGAAGCCCAGCCCCCCGCAGTTCTCCATACAGTGGCCTTACTACG
TCCTGGGCTTCAGCATCCTTCTGTTCATGGTGGCTGGTGCCATCTGCCTCATCCAAGAAATAGCCTGCCCTAGATGCCAT
TTGTTGCCCATTTCCCAGAGTACTGAGGACACCCAAGAGATCTCGTACCTGGAAAACCTGGATAGTCTGGGAGGAGAACT
GAGCTCCATGCAGAAGGAGACGCTGCTGAAGGAAGAAACCATTATC

Alignment

ORF - retro_btau_458 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.01 %
• Parental protein coverage: 89.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTSLGYLLILLVSIFPFWVRLVNEESQEVFFSGLFENCFHIKCWKPRPLSIYVILGRVSLLSAVVLSFLT
          ..SLGYLLILLVSIFPFWVRLVNEESQEVFFSGLFENCFHIKCWKPRPLSIYVILGRVSLLSAVVLSFLT
Retrocopy VASLGYLLILLVSIFPFWVRLVNEESQEVFFSGLFENCFHIKCWKPRPLSIYVILGRVSLLSAVVLSFLT

Parental  TFIMVSFASQLFPRTRKHNFVSAFISFLTGACAFLALLLHALEIQSLRMKPSPPQFSIQWPYYVLGFSIL
          TFIMVSFASQLFPRTRKHNFVSAFISFLTGACAFLALLLHALEIQSLRMKPSPPQFSIQWPYYVLGFSIL
Retrocopy TFIMVSFASQLFPRTRKHNFVSAFISFLTGACAFLALLLHALEIQSLRMKPSPPQFSIQWPYYVLGFSIL

Parental  LFMVAGAICLIQEIACPRCHLLPISQSTEDTQEISYLENLDSLGGELSSMQKETLLKEETII
          LFMVAGAICLIQEIACPRCHLLPISQSTEDTQEISYLENLDSLGGELSSMQKETLLKEETII
Retrocopy LFMVAGAICLIQEIACPRCHLLPISQSTEDTQEISYLENLDSLGGELSSMQKETLLKEETII

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	1.87 RPM
ERP005899_muscle	0.05 RPM	4.91 RPM
SRP017611_brain	0.09 RPM	5.25 RPM
SRP017611_kidney	0.06 RPM	5.51 RPM
SRP017611_liver	0.08 RPM	1.21 RPM
SRP030211_testis	0.95 RPM	66.06 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_458 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039720	2 retrocopies	retro_btau_1081, retro_btau_458 ,