RetrogeneDB ID: retro_vpac_540

Retrocopy location

• Organism: Alpaca (Vicugna pacos)
• Coordinates: scaffold_37901:3216..4110(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1CC
• Ensembl ID: ENSVPAG00000008411
• Aliases: None
• Description: protein phosphatase 1, catalytic subunit, gamma isozyme [Source:HGNC Symbol;Acc:9283]

Sequence

>retro_vpac_540
ATGGCAGGTAGAGATAAACTCCACATGAACAGCATCATCCAATGGCTGCTGGAAGTGAGAGGCTCCAAGCCGCATAAGAA
TGTCCAGCTTCAAAATGAAATCAGAGTACTCTGCTTAAATTCCTGAGAGATCTTTCTCAGTCCACCAATCCTACAACAGC
TTGAAACACCACTCAAATCATGTGATGATACCCACCAGCAATACTATGATTTGCTTCAACTTTTGGAGTACAGTGTGGTT
TTCCACCAGAAAGCAAGTCCTTTTTTTTGGAAACTATGTGGACAAGGAGAAACAGTCTTTGGAGACTATCTGCCTCTTAT
TGACTAAGAATAACAAATATCCCAAGAATAGTTTTCATCTCAGACGAAACCACGAATGTGCCGGCATCAATAGAGTGTAT
GAATTTTACGATGGATGTAAAAGAAGGTACAACATTACACTGCGGAAAACTTTCATGGAGTGCTTTAACTGCTACTGATG
GCAGCCATCATGAACGAGAAAATAGTATGCTGTCATGGAAGTTTATCACCAGATCTTGAATCTGTACAGCAGGTTCCAAA
AACTATATGACCAACTGATGTACCAGATCAAGGTCTTTGTAATCTTTTGTGCTCTGACCCAGATAAAGATGTCTTAGGCT
GGGGTGAAAATGACAGAGAGGTGTCCTGGTGTCCTTCACGTTTGGTGCAGAAGTGGTTGCAAAATTTCTCCATAAGCATG
ATTTGGATCATCAAGTGGTTGAAGAGGGATGTATATTTTTGCAAAGAGGCAGTTGGTCACTGTTTTTCTGCACCTGATTA
TTGTGGAGAGTTTGACACTGGAGGTGCCATGATGAATGTGGACAAAACACTAATGTGTTCTTCTCAGATTTTAAAGCCTA
CAGAGAAAAAGGAG

Alignment

ORF - retro_vpac_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.62 %
• Parental protein coverage: 89.91 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADIDKLNIDSIIQRLLEVRGSKPGKNVQLQENEIRGLCLKSREIFLSQPILLELEAPLKICGDIHGQYY
          MA..DKL...SIIQ.LLEVRGSKP.KNVQLQ.NEIR.LCL.S.EIFLS.PIL..LE.PLK.C.D.H.QYY
Retrocopy MAGRDKLHMNSIIQWLLEVRGSKPHKNVQLQ-NEIRVLCLNS*EIFLSPPILQQLETPLKSCDDTHQQYY

Parental  DLLRLFEYG-GFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYPENFFLLRGNHECASINRIYGFYDE
          DLL.L.EY...F.........G.YVD..KQSLETICLLL....KYP.N.F.LR.NHECA.INR.Y.FYD.
Retrocopy DLLQLLEYS>WFSTRKQVXXXGNYVDKEKQSLETICLLLTKNNKYPKNSFHLRRNHECAGINRVYEFYDG

Parental  CKRRYNIKLWKTFTDCFNC-LPIAAIVDEKIFCCHGGLSPDLQSMEQIRRIMRPTDVPDQGLLCDLLWSD
          CKRRYNI.L.KTF..CFNC.L..AAI..EKI.CCHG.LSPDL.S..Q......PTDVPDQG.LC.LL.SD
Retrocopy CKRRYNITLRKTFMECFNC<LLMAAIMNEKIVCCHGSLSPDLESVQQVPKTI*PTDVPDQG-LCNLLCSD

Parental  PDKDVLGWGENDRGVSFTFGAEVVAKFLHKHDLDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDN
          PDKDVLGWGENDR.VS.......V.K.L.......I........D.Y..F.K......FSAP.YCGEFD.
Retrocopy PDKDVLGWGENDREVSWC-PSRLVQKWLQNFSISMIWIIKWLKRDVY--FCKEAVGHCFSAPDYCGEFDT

Parental  AGAMMSVDETLMCSFQILKPAEKKK
          .GAMM.VD.TLMCS.QILKP.EKK.
Retrocopy GGAMMNVDKTLMCSSQILKPTEKKE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq

Vicugna pacos was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_vpac_540 retrocopy.

TSS

Vicugna pacos was not studied using FANTOM5 data.

Lab

retro_vpac_540 was not experimentally validated.

Homology

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Dipodomys ordii	ENSDORG00000010484	2 retrocopies	retro_dord_260, retro_dord_261,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Vicugna pacos	ENSVPAG00000008411	1 retrocopy	retro_vpac_540 ,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21, retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,