RetrogeneDB ID: retro_btau_494

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:33647817..33648405(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000016116
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MARCKSL1
• Ensembl ID: ENSBTAG00000046862
• Aliases: None
• Description: MARCKS-related protein [Source:RefSeq peptide;Acc:NP_001069640]

Sequence

>retro_btau_494
ATGGGCAGCCAGAGCTCCAAGGCTCCCCGGGGCGACGTGACCGCCGAGGAGGCAGCAGGCGCTTCCCCCGCCAAGGTCAA
CGGACAGGAGAACGGCCACGTGAAAAGCAATGGAGACATCCCCCAAAGGTGAAGGGGAGTCGCCCCCGTGAACGGAACAG
AGGAGGCAGCGGGGGCCACTGGTGATGCTATCGAGCCAGCACCCCCTAGCCAGGGCGCTGAGGCTAAGGGGGAGGTCCCC
CCCAAGGAGACCCCCAAGAAGAAGAAGAAATTCTCTTTCAAGAAGCCTTTCAAATTGAGTGGCCTGTCCTTCAAGAGAAA
TCGGAAGGAGGGTGGGGGTGATTCGTCTGCCTCCTCACCCACAGAGGAAGAGCAGGAGCAGGGGGAGATCAGTGCCTGCG
GCGAGGAGGGCACTGCCCAGGAAGGGAAGGCTGCTGCCATCCCCGAGAGCCAGGAGCCTCAGGCCAAAGGGGCAGAGGCC
AGCCCTACCGTCAAGGGAGACACAGAAGAGGCAGGGCCCCAGGCCGCAGAGCCATCCACTCCCTCGGGGCCAGAGAGTGA
CCCTGCACCAGCCAGCGAGCAGAATGAG

Alignment

ORF - retro_btau_494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGSQSSKAPRGDVTAEEAGGAAIERAPGEENGHVKSNGDL-SPK-GEGESP-PVNGTEEAAGATGDAIEP
          MGSQSSKAPRGDVTAEEA.GA......G.ENGHVKSNGD...PK.GEGESP.PVNGTEEAAGATGDAIEP
Retrocopy MGSQSSKAPRGDVTAEEAAGASPAKVNGQENGHVKSNGDI<PPK<GEGESP<PVNGTEEAAGATGDAIEP

Parental  APPSQGAEAKGEVPPKETPKKKKKFSFKKPFKLSGLSFKRNRKEGGGDSSASSPTEEEQEQGEISACGEE
          APPSQGAEAKGEVPPKETPKKKKKFSFKKPFKLSGLSFKRNRKEGGGDSSASSPTEEEQEQGEISACGEE
Retrocopy APPSQGAEAKGEVPPKETPKKKKKFSFKKPFKLSGLSFKRNRKEGGGDSSASSPTEEEQEQGEISACGEE

Parental  GTAQEGKAAATPESQEPQAKGAEASAAAKGGDTEEAGPQAAEPSTPSGPESDPAPASEQNE
          GTAQEGKAAA.PESQEPQAKGAEAS...K.GDTEEAGPQAAEPSTPSGPESDPAPASEQNE
Retrocopy GTAQEGKAAAIPESQEPQAKGAEASPTVK-GDTEEAGPQAAEPSTPSGPESDPAPASEQNE

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	0.50 RPM
ERP005899_muscle	0.90 RPM	7.28 RPM
SRP017611_brain	17.36 RPM	58.01 RPM
SRP017611_kidney	0.30 RPM	2.19 RPM
SRP017611_liver	0.68 RPM	1.74 RPM
SRP030211_testis	3.62 RPM	14.75 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_494 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_494 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_494 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	ENSBTAG00000046862	2 retrocopies	retro_btau_494 , retro_btau_921,