RetrogeneDB ID: retro_btau_1103

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 26:29342065..29342485(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP4B
• Ensembl ID: ENSBTAG00000013387
• Aliases: None
• Description: charged multivesicular body protein 4b [Source:RefSeq peptide;Acc:NP_001121978]

Sequence

>retro_btau_1103
ACGCTGTCAACAATCGAGTTCCAGCGAGAGGCCCTGGAGAATGCCAACACCAACACCGAGGTGCTCAAGAACATGGGCTA
TGCCGCCAAGGCCATGAAGGCTGCCCACGACAACATGGACATCGACAAAGTTGATGAGTTAATGCAGGACATTGCTGACC
AGCAGGAACTTGCAGAAGAGATTTCAACAGCTATTTCAAAACCCGTAGGGTTTGGAGAAGAGTTTGATGAGGATGAGCTC
ATGGCAGAATTAGAAGAACTAGAACAGGAGGAACTAGATAAGAATTTGCTGGAAATCAGTGGACCGGAAACAGTCCCTCT
ACCGAGTGTTCCCTCTATATCCCTACCATCAAAACCCGCCAAGAAGAAGGAAGAAGAAGACGACGACATGAAGGAATTAG
AGACCTGGGCTGGAACCATT

Alignment

ORF - retro_btau_1103 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.29 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQELAEEISTAISKPVG
          TLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQELAEEISTAISKPVG
Retrocopy TLSTIEFQREALENANTNTEVLKNMGYAAKAMKAAHDNMDIDKVDELMQDIADQQELAEEISTAISKPVG

Parental  FGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPSVPSISLPSKPAKKKEEEDEDMKELETWAGTI
          FGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPSVPSISLPSKPAKKKEEED.DMKELETWAGTI
Retrocopy FGEEFDEDELMAELEELEQEELDKNLLEISGPETVPLPSVPSISLPSKPAKKKEEEDDDMKELETWAGTI

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	10.53 RPM
ERP005899_muscle	0.11 RPM	67.83 RPM
SRP017611_brain	0.32 RPM	54.36 RPM
SRP017611_kidney	0.30 RPM	37.82 RPM
SRP017611_liver	0.08 RPM	18.27 RPM
SRP030211_testis	0.36 RPM	40.18 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1103 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013387	1 retrocopy	retro_btau_1103 ,
Gorilla gorilla	ENSGGOG00000007775	1 retrocopy	retro_ggor_29,
Rattus norvegicus	ENSRNOG00000046585	1 retrocopy	retro_rnor_61,