RetrogeneDB ID: retro_btau_1199

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 29:40307156..40307637(-)
• Located in intron of: None

Retrocopy information

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

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_1199
CATGTCTGGAAATATTTTACAGATCTTTTTGACCATCTTCCTCTCACTGCCTCAGTGGCTGGGCAGATAGTCTGTCTACA
TGGTGGCCTCTCACCATCCATAGATACACTGGATCACATCAGAGCTCTTGATCACTTACGAGAAGTTCCCCACGAGGGTC
CAACGTATCACTTGCTGTGGTCAGATCCAGAGGGACCATGGAGATTGGGGTATATCTCCTCAAGGAGCTGACTACACCTT
TGGGCAGGATGTTTCTGAGACATTTAATCATGCCAATGGCCTCCTGTTGGTGTGTAGAGCTCATTGGCTGGTGATGGAGG
GATATAACTGGTGTTTTGCCTGAAATGCAGTAACGATTTTCAGTGCTCCAAAATATTGTTATTGTTGTGGTAACCAAGCT
GCAATCTTGGAACTTGATGATACTCTAAAATACTCTTTCTTGCAGATTGACCCAGCCGCTCACAGAGGCAAGCCACATGT
T

Alignment

ORF - retro_btau_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.75 %
• Parental protein coverage: 51.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPD-DRGGW
          .VWKYFTDLFD.LPLTA.V.GQI.CLHGGLSPSIDTLDHIRALD.L.EVPHEGP...LLWSDP..D.G.W
Retrocopy HVWKYFTDLFDHLPLTASVAGQIVCLHGGLSPSIDTLDHIRALDHLREVPHEGPTYHLLWSDPE>DHGDW

Parental  GISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELD
          GISP.GA.YTFGQD.SETFNHANGL.LV.RAH.LVMEGYNWC...N.VTIFSAP.YCY.CGNQAAI.ELD
Retrocopy GISPQGADYTFGQDVSETFNHANGLLLVCRAHWLVMEGYNWCFA*NAVTIFSAPKYCYCCGNQAAILELD

Parental  DTLKYSFLQFDPAPRRGEPHV
          DTLKYSFLQ.DPA..RG.PHV
Retrocopy DTLKYSFLQIDPAAHRGKPHV

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	62.87 RPM
ERP005899_muscle	0.00 RPM	30.67 RPM
SRP017611_brain	0.00 RPM	52.99 RPM
SRP017611_kidney	0.00 RPM	30.35 RPM
SRP017611_liver	0.00 RPM	18.65 RPM
SRP030211_testis	0.00 RPM	35.03 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1199 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1199 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1199 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,