RetrogeneDB ID: retro_btau_1754

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:90724319..90724786(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CA
• Ensembl ID: ENSBTAG00000000469
• Aliases: None
• Description: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [Source:UniProtKB/Swiss-Prot;Acc:P67774]

Sequence

>retro_btau_1754
ATGGATGAGAAGGTGTTCACCAAGGAGCTGACCAGTGGACCAAGCAGCTGAACAAGTGCAAGCAGCTGTCCCAGCCCCAG
GTCAAGAGCCTCCGTGAGAAGGCTAACGAAATCCTGACAAAAGAATCCAATGTGCAAGTCGTTCGATGTCTAGTCATCGT
CTGTAGAGATGTGCATGGGAAATTTCAGGATCTCATGGAATTGTTTAGAATTGGTGGCACATCACCAGATACGAATTACT
TGTTTATGGGCAATTATTTTGACAGAGGATATCATTCAGTGAAAACAGTTAATCTGCTTGTAGCTCTTAAGGTTCATTAC
CATGAATGTATCACCTTTCTTCAGGGAAATCATGAGAGCAGACAGATCACACAAGTACATGGTTTCTATGATGAGTGTTT
AAGAAACTACAGAAATGCAACTGTTTAGAAATATTTTACAGATCTTTTTGACTATCTTCCTATCACT

Alignment

ORF - retro_btau_1754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 50.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDEKVFTKEL-DQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELF
          MDEKVFTKEL.DQW..QLN.CKQLS..QVKSL.EKA.EILTKESNVQ.VRC.V.VC.DVHG.F.DLMELF
Retrocopy MDEKVFTKEL<DQWTKQLNKCKQLSQPQVKSLREKANEILTKESNVQVVRCLVIVCRDVHGKFQDLMELF

Parental  RIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGN
          RIGG.SPDTNYLFMG.Y.DRGY.SV.TV.LLVALKV.Y.E.IT.L.GNHESRQITQV.GFYDECLR.Y.N
Retrocopy RIGGTSPDTNYLFMGNYFDRGYHSVKTVNLLVALKVHYHECITFLQGNHESRQITQVHGFYDECLRNYRN

Parental  ANVWKYFTDLFDYLPLT
          A.V.KYFTDLFDYLP.T
Retrocopy ATV*KYFTDLFDYLPIT

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	105.76 RPM
ERP005899_muscle	0.00 RPM	141.53 RPM
SRP017611_brain	0.00 RPM	169.15 RPM
SRP017611_kidney	0.00 RPM	138.64 RPM
SRP017611_liver	0.00 RPM	54.74 RPM
SRP030211_testis	0.00 RPM	78.72 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1754 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000002653	1 retrocopy	retro_acar_69,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754 ,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704,
Dasypus novemcinctus	ENSDNOG00000013011	4 retrocopies	retro_dnov_1025, retro_dnov_1844, retro_dnov_2100, retro_dnov_2122,
Echinops telfairi	ENSETEG00000007561	2 retrocopies	retro_etel_1233, retro_etel_659,
Felis catus	ENSFCAG00000029685	1 retrocopy	retro_fcat_1086,
Mustela putorius furo	ENSMPUG00000010169	1 retrocopy	retro_mputfur_633,
Sorex araneus	ENSSARG00000005447	3 retrocopies	retro_sara_296, retro_sara_385, retro_sara_715,
Sarcophilus harrisii	ENSSHAG00000016632	3 retrocopies	retro_shar_313, retro_shar_428, retro_shar_471,
Tursiops truncatus	ENSTTRG00000016859	1 retrocopy	retro_ttru_1584,