RetrogeneDB ID: retro_btau_960

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 21:47842362..47843263(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSBTAG00000011198
• Aliases: None
• Description: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit [Source:UniProtKB/Swiss-Prot;Acc:P61287]

Sequence

>retro_btau_960
GCAGATATAAATAAACTCAATATTGGTGGTAACATCTAACTGCTGCTGTAAGTGAGAGAGTCCAAGCCTAGTAAGAATGT
CTAGCTACAGGAGAATGAAATCAGAGGACTGTGCTTAAAGTCCCAAGAGAGCTTTCTCAATCTGTCTTATCCTGCTAGAA
CTTGAAGCACCACTCAAGATACGTGGTGATATCCATGGGCAATACTACGATTTTCTTCGAGTTTTTGAGTAGAGTGGTGC
CATCCGGCCAGAAAGCAATTACCTGTTTATTGGGGACTATGCACATAGGGGAAAGCAGTCATTGGAGACTATCAGCCTCT
TGTTGGCTTACAAAATCAAATATCCTGAGAAATTTTTTCTTCTCAGAGGAAACCATGAATGTGCCAGCATCAATAGAATT
TATGGATTTTATGGTGAGTGTAAAAGAAGATATAACATTAAACTATGGAAAACTTTCACAGCCTGCTTTAACTGTTTACT
GATAGCAGACATTGCGGATGAGAAAATATTCTGCTGTCATGGAGGTTTATCACCAAATCTTCAATCCATGAAACAGATTT
GGCGAATTATGTGACCAACTGATGTACAAGATCAAGGTCTTCTTTGTGATCTTTTGTGGTCTGACCCCGATGAAGATGTC
TTAAGCTGGGGTGAAAATGACAGAGGAGTGTCCACATTTGATGCAGAAGTGGTTGTAAAATTTCTCCATAGGCATAATTT
GGATCTTATATGTAAAGCCCATTAAGTGGTTGAAGATGGATATGAATTTTTTGCAAAGAGGCAGTTGGTCACTCTGTTTT
CCGTGCCCAATTATTGTAGGGAGTTTGACAATGCAGGTACCATGATAAGTGTGGACGAAACACATCTGATGTGTTCTTTT
CAGATTTTAAAGCCTACAGAG

Alignment

ORF - retro_btau_960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 92.57 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQP-ILLELEAPLKICGDIHGQYY
          ADI.KLNI...I..LL.VR.SKP.KNV.LQENEIRGLCLKS.E.FL....ILLELEAPLKI.GDIHGQYY
Retrocopy ADINKLNIGGNI*LLL*VRESKPSKNV*LQENEIRGLCLKSQESFLNLS>ILLELEAPLKIRGDIHGQYY

Parental  DLLRLFE-YGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDE
          D.LR.FE..G...PESNYLF.GDY..RGKQSLETI.LLLAYKIKYPE.FFLLRGNHECASINRIYGFY.E
Retrocopy DFLRVFE*SGAIRPESNYLFIGDYAHRGKQSLETISLLLAYKIKYPEKFFLLRGNHECASINRIYGFYGE

Parental  CKRRYNIKLWKTFTDCFNCLPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSDP
          CKRRYNIKLWKTFT.CFNCL.IA.I.DEKIFCCHGGLSP.LQSM.QI.RIM.PTDV.DQGLLCDLLWSDP
Retrocopy CKRRYNIKLWKTFTACFNCLLIADIADEKIFCCHGGLSPNLQSMKQIWRIM*PTDVQDQGLLCDLLWSDP

Parental  DKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNA
          D.DVL.WGENDRGVS.TF.AEVV.KFLH.H.LDLIC.AH.VVEDGYEFFAKRQLVTLFS.PNYC.EFDNA
Retrocopy DEDVLSWGENDRGVS-TFDAEVVVKFLHRHNLDLICKAH*VVEDGYEFFAKRQLVTLFSVPNYCREFDNA

Parental  GAMMSVDET-LMCSFQILKPAE
          G.M.SVDET.LMCSFQILKP.E
Retrocopy GTMISVDETHLMCSFQILKPTE

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	50.54 RPM
ERP005899_muscle	0.00 RPM	71.74 RPM
SRP017611_brain	0.00 RPM	57.74 RPM
SRP017611_kidney	0.00 RPM	60.16 RPM
SRP017611_liver	0.00 RPM	28.54 RPM
SRP030211_testis	0.06 RPM	339.38 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_960 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6, retro_btau_960 ,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,