RetrogeneDB ID: retro_btau_947

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:14630145..14630556(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000047409
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BT.66169
• Ensembl ID: ENSBTAG00000023938
• Aliases: CENPA, CENP-A
• Description: histone H3-like centromeric protein A [Source:RefSeq peptide;Acc:NP_001192309]

Sequence

>retro_btau_947
GGACCCAGAAGATCTAGGAGCCACGGGGCCGCAAGCCCGAAACACCAAGGAGGCGGGGGCCCCGCGAGTCCGGCTCCGCC
GCCCGCCGGCTGGCGCGTCCTCCGTCCGCTTGCTCGCCGGAGACATGGAATCCTGAAGGAGGGCCGAGCTCTTCAAAAGA
CCACACACCTGCTGTTAAGAAAGTCCCCCTTCTGCCGCCTGGCAAGAGAAATCTGTGTTCAGTTCACTCGCGGTGTGGAC
TTCAGTTGGCAAGCCCAGGCCCTGTTGGCCCTACAAGAGGCGGCAGAAGCGTTTCTAGTTCATTTCTTCGAGGATGCCTA
TCTGCTCTCCTTACACGCCGGCCGCATCACACTCTTCTCGAAGGATGTGCAGCTGGCCCGGAGGATCCGAGGCATTCAGG
AAGGGCTGGGC

Alignment

ORF - retro_btau_947 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPRRHKRKPETPRRRPASPAPAAPRPTPSLGTSSRPLARRRHTVLKEIRTLQKTTHLLLRKSPFCRLARE
          GPRR................PA.P.P.P......RPLARRRH..LKE.R.LQKTTHLLLRKSPFCRLARE
Retrocopy GPRRSRSHGAASPKHQGGGGPASPAPPPAGWRVLRPLARRRHGILKEGRALQKTTHLLLRKSPFCRLARE

Parental  ICVQFTRGVDFNWQAQALLALQEAAEAFLVHLFEDAYLLSLHAGRVTLFPKDVQLARRIRGIQEGLG
          ICVQFTRGVDF.WQAQALLALQEAAEAFLVH.FEDAYLLSLHAGR.TLF.KDVQLARRIRGIQEGLG
Retrocopy ICVQFTRGVDFSWQAQALLALQEAAEAFLVHFFEDAYLLSLHAGRITLFSKDVQLARRIRGIQEGLG

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	1.44 RPM
ERP005899_muscle	0.00 RPM	7.76 RPM
SRP017611_brain	0.00 RPM	0.18 RPM
SRP017611_kidney	0.06 RPM	1.01 RPM
SRP017611_liver	0.15 RPM	0.00 RPM
SRP030211_testis	0.02 RPM	3.81 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_947 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_947 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_947 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000023938	1 retrocopy	retro_btau_947 ,
Choloepus hoffmanni	ENSCHOG00000004496	3 retrocopies	retro_chof_2096, retro_chof_2448, retro_chof_4,
Ornithorhynchus anatinus	ENSOANG00000000516	1 retrocopy	retro_oana_72,
Otolemur garnettii	ENSOGAG00000024154	2 retrocopies	retro_ogar_3405, retro_ogar_3505,
Ictidomys tridecemlineatus	ENSSTOG00000025168	2 retrocopies	retro_itri_835, retro_itri_994,
Tarsius syrichta	ENSTSYG00000010334	1 retrocopy	retro_tsyr_2007,
Tursiops truncatus	ENSTTRG00000010278	2 retrocopies	retro_ttru_590, retro_ttru_784,