RetrogeneDB ID: retro_btau_571

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 15:13987257..13987767(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009511
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP1R14C
• Ensembl ID: ENSBTAG00000026586
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14C [Source:RefSeq peptide;Acc:NP_001071536]

Sequence

>retro_btau_571
ATGTCGGTGGCGACGGGCAGCAGCGAGGCGGCCGGCGGGGCCGCGGGCAGCGGTGCGCGGGTTTTCTTCCAGAGTCCCCG
GGGCGGTGCCAGCGGCAGCCCGGGCTCGAGCAGCGGCTCGGGCTCCTCCCCGGAGGACTCGGCGCCCGTGGCCACCGCGG
CTCCCGCCGGGCACGTTCAGCAGCAGCAGCAGCAGCAGCAGCAACAGCGGCGCCACCAGCAGGGAAAAGTGACGGTAAAA
TACGATCGCAAGGAGCTTCGGAAACGGCTCGTGCTGGAGGAGTGGATCGTGGAGCAGCTGGGACAGCTGTATGGCTGCGA
GGAAGAAGAAATGCCAGATGTGGAAATTGACATTGATGATCTTCTTGATGCAGACAGTGAAGAAGAGAGGGCTTTAAAAT
TACGAGAAGCTCTTGTAGACTGCTACAAACCAACAGAGGAGTTCATTAAGGAGCTGCTCTCTCGGATAAGAGGCATGCGA
AAGTTGAGCCCCCCACAGAAGAAGGCTGTA

Alignment

ORF - retro_btau_571 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVATGSSEAAGGAAGSGARVFFQSPRGGASGSPGSS--SGSGSSREDSAPVATAAPAGHVQQQQQQQQR
          MSVATGSSEAAGGAAGSGARVFFQSPRGGASGSPGSS..SGS..........A..A..............
Retrocopy MSVATGSSEAAGGAAGSGARVFFQSPRGGASGSPGSSSGSGSSPEDSAPVATAAPAGHVXXXXXXXXXXX

Parental  RHQQGKVTVKYDRKELRKRLVLEEWIVEQLGQLYGCEEEEMPDVEIDIDDLLDADSEEERALKLREALVD
          RHQQGKVTVKYDRKELRKRLVLEEWIVEQLGQLYGCEEEEMPDVEIDIDDLLDADSEEERALKLREALVD
Retrocopy RHQQGKVTVKYDRKELRKRLVLEEWIVEQLGQLYGCEEEEMPDVEIDIDDLLDADSEEERALKLREALVD

Parental  CYKPTEEFIKELLSRIRGMRKLSPPQKKAV
          CYKPTEEFIKELLSRIRGMRKLSPPQKKAV
Retrocopy CYKPTEEFIKELLSRIRGMRKLSPPQKKAV

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.11 RPM
SRP017611_brain	0.14 RPM	3.84 RPM
SRP017611_kidney	0.18 RPM	6.40 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.01 RPM	0.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_571 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023472	1 retrocopy	retro_btau_282,
Bos taurus	ENSBTAG00000026586	2 retrocopies	retro_btau_161, retro_btau_571 ,
Dasypus novemcinctus	ENSDNOG00000017261	2 retrocopies	retro_dnov_1661, retro_dnov_80,
Myotis lucifugus	ENSMLUG00000023245	2 retrocopies	retro_mluc_1095, retro_mluc_499,
Mus musculus	ENSMUSG00000040653	2 retrocopies	retro_mmus_2089, retro_mmus_3721,
Pongo abelii	ENSPPYG00000017102	4 retrocopies	retro_pabe_1880, retro_pabe_2079, retro_pabe_3001, retro_pabe_3232,
Tarsius syrichta	ENSTSYG00000002873	1 retrocopy	retro_tsyr_245,