RetrogeneDB ID: retro_btau_689

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:14983422..14983950(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000025283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.87557
• Ensembl ID: ENSBTAG00000010545
• Aliases: KXD1, C19orf50, C7H19orf50
• Description: UPF0459 protein C19orf50 homolog [Source:RefSeq peptide;Acc:NP_001029777]

Sequence

>retro_btau_689
ATGGACCCCCCGGACTCGGCCTCGAGGGTCTTCTGTAGCCGCATCCTGAGCATGGTTAATGCGGACGATGTCAGTGCCAT
CATCCTGGCCCAGAAGAACATGCTGGACCGCTTTGAAAAGACCAACGAGATGCTGCTCAACTTCAACAACCTGTCAAGTG
CCCGCCTGCAGCAGATGAACGAGCGCTTCCTGCACCACACAAGGACCCTGGTGAAGATGAAACGGAACTTGGACAGCATC
TTCCGCAGGATCAGGACACTGAAAGGGAAGCTGGCCAGACAGCACCCGGAGGCCTTCAGCCACATCCCAGAGGCATCTCT
CCTGGAGGACGAAGATGAAGACCCCATTCCGCCTAGCACCACCACCACCATCGCCACCTCAGAACAGAGCACAGGCTCAT
GTGACACCAGTCCCGACACTGTCTCGCCCTCCCTCAGCCCTGGCTTCGAGGACCTGTCCCACATCCGGCCTGGTTCCCCT
GCCATCAATGGTCGCAGCCATACAGATGACGAGGAGATGCCGGGCGAG

Alignment

ORF - retro_btau_689 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDPPDSASRVFCSRILSMVNADDVSAIILAQKNMLDRFEKTNEMLLNFNNLSSARLQQMNERFLHHTRTL
          MDPPDSASRVFCSRILSMVNADDVSAIILAQKNMLDRFEKTNEMLLNFNNLSSARLQQMNERFLHHTRTL
Retrocopy MDPPDSASRVFCSRILSMVNADDVSAIILAQKNMLDRFEKTNEMLLNFNNLSSARLQQMNERFLHHTRTL

Parental  VEMKRDLDSIFRRIRTLKGKLARQHPEAFSHIPEASLLEDEDEDPIPPSTTTTIATSEQSTGSCDTSPDT
          V.MKR.LDSIFRRIRTLKGKLARQHPEAFSHIPEASLLEDEDEDPIPPSTTTTIATSEQSTGSCDTSPDT
Retrocopy VKMKRNLDSIFRRIRTLKGKLARQHPEAFSHIPEASLLEDEDEDPIPPSTTTTIATSEQSTGSCDTSPDT

Parental  VSPSLSPGFEDLSHIRPGSPAINGRSHTDDEEMPGE
          VSPSLSPGFEDLSHIRPGSPAINGRSHTDDEEMPGE
Retrocopy VSPSLSPGFEDLSHIRPGSPAINGRSHTDDEEMPGE

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	19.25 RPM
ERP005899_muscle	0.05 RPM	31.15 RPM
SRP017611_brain	0.18 RPM	32.30 RPM
SRP017611_kidney	0.00 RPM	29.04 RPM
SRP017611_liver	0.00 RPM	21.97 RPM
SRP030211_testis	0.13 RPM	40.11 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_689 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_689 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_689 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010545	1 retrocopy	retro_btau_689 ,
Echinops telfairi	ENSETEG00000003390	2 retrocopies	retro_etel_1213, retro_etel_2129,
Macropus eugenii	ENSMEUG00000013150	1 retrocopy	retro_meug_2148,
Monodelphis domestica	ENSMODG00000003489	1 retrocopy	retro_mdom_1623,
Mus musculus	ENSMUSG00000055553	6 retrocopies	retro_mmus_1117, retro_mmus_3557, retro_mmus_799, retro_mmus_800, retro_mmus_802, retro_mmus_804,
Rattus norvegicus	ENSRNOG00000019971	2 retrocopies	retro_rnor_2808, retro_rnor_812,