RetrogeneDB ID: retro_btau_704

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:50368467..50369395(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000037966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSBTAG00000009245
• Aliases: None
• Description: Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [Source:UniProtKB/Swiss-Prot;Acc:Q0P594]

Sequence

>retro_btau_704
ATGGACGACAAGGCGTTCACTAAGGACCTGGACCAGTGGGTCGAGCAGCTGAATGAGTGTACAACAGCTGAACGAGAACC
AAGTCCGGACGCTGTGTGAAAAGGCTAAGGAAATTTTAACAAAAGAATCGAATGTACAGGAGGTCCGTTGTCCTGTCACC
GTCTGTGGAGATGTGCATGGCCAGTTCCACGACCTTATGGAACTCTTCAGAATCGGTGGGAAGTCACCAGACACAAACTA
TCTGTTCATGGGCGACTGTGTAGACAGAGGTTATTATTCTGTGGAAACGGTAACTCTTCTTGTGGCATTAAAGGTGCGTT
ATCCAGAGCGCATTACAATACTGAGAGGAAACCACGAAAGCCGACAAATTACCCAAGTTTATGGCTTTTATGACGAATGT
CTGCGAAAGTATGGAAATGCCAATGTTTGGAAATATTTTACAGATCTCTTTGATTATCTGCCACTTACAGCTTTAGTAGA
TGGACAGATATTCTGCCTCCATGGTGGCCTCTCTCCATCCATAGATACACTGGATCATATAAGAGCCCTGGATCGTTTAC
AAGAAGTTCCACATGAGGGCCCTATGTGTGATCTCTTATGGTCAGATCCAGATGATCGTGGTGGGTGGGGTATTTCTCCA
CGTGGTGCTGGCTACACATTTGGACAAGATATTTCTGAAACGTTTAACCATGCTAATGGTCTCACACTGGTTTCTCGTGC
TCACCAACTTGTAATGGAGGGATACAATTGGTGTCACGATCGGAACGTGGTTACCATTTTCAGTGCACCCAATTACTGTT
ATCGTTGTGGGAACCAGGCTGCTATCATGGAATTAGATGACACTTTGAAATATTCCTTCCTTCAGTTTGACCCAGCACCT
CGTCGTGGAGAGCCTCATGTGACCCGGCGCACCCCAGACTACTTCCTG

Alignment

ORF - retro_btau_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.03 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDDKAFTKDLDQWVEQLNEC-KQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELF
          MDDKAFTKDLDQWVEQLNEC..QLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELF
Retrocopy MDDKAFTKDLDQWVEQLNEC>QQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELF

Parental  RIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGN
          RIGGKSPDTNYLFMGD.VDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGN
Retrocopy RIGGKSPDTNYLFMGDCVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGN

Parental  ANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGW
          ANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGW
Retrocopy ANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGW

Parental  GISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELD
          GISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELD
Retrocopy GISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELD

Parental  DTLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          DTLKYSFLQFDPAPRRGEPHVTRRTPDYFL
Retrocopy DTLKYSFLQFDPAPRRGEPHVTRRTPDYFL

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	0.29 RPM	62.87 RPM
ERP005899_muscle	0.16 RPM	30.67 RPM
SRP017611_brain	0.50 RPM	52.99 RPM
SRP017611_kidney	0.24 RPM	30.35 RPM
SRP017611_liver	0.30 RPM	18.65 RPM
SRP030211_testis	0.20 RPM	35.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_704 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_704 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_704 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001615	1 retrocopy	retro_amel_663,
Bos taurus	ENSBTAG00000000469	1 retrocopy	retro_btau_1754,
Bos taurus	ENSBTAG00000009245	3 retrocopies	retro_btau_1199, retro_btau_1750, retro_btau_704 ,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Echinops telfairi	ENSETEG00000018123	4 retrocopies	retro_etel_1607, retro_etel_1923, retro_etel_680, retro_etel_702,
Felis catus	ENSFCAG00000025139	1 retrocopy	retro_fcat_1884,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Otolemur garnettii	ENSOGAG00000002488	1 retrocopy	retro_ogar_3188,
Tursiops truncatus	ENSTTRG00000000102	1 retrocopy	retro_ttru_1576,