RetrogeneDB ID:

retro_cpor_644

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_21:13374490..13375151(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAZ
Ensembl ID:ENSCPOG00000020285
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_644
TATAATGCCATGGCAGCCCATGTGAAGTCTGTATCTGAGCAAGGCACTGGATTATCTAATGAGGAGAGGAATCTTCTCTG
TGTTCTTCAAAAAATGTTACAGGAGCCTATAGTTCATCTTGGAAGGTTGTCTCAAGCACTGAGCAAAAGATGGAAGGTGC
TGAGACAGGGCAGCAGATGGCTCAAGAACACAGAGAGAAAACTGAGGCTGAGCTAAGGCTTACCTGCAACAATGTACTAT
CTCTTTTGGAAAAGTTCTTGATCCCCAGTGCTTCACAAGCAGAGAGCAGCATTTTATTTGAAAACGAAAGGAGACTACTA
CTGTTATTGTCTGGGGTTGCTGCTGGTGATGACCAGAAAGGGATTGTGGGGCAGTCACAACAAAGATACCAAAAGTTTTT
GAAATCAGGATAAAGGAAATGCAACCAATGCATCCTATCAGATTGAGTCTGACCCTCAACTACTCTATGTTTTATTATGA
GATTCTGAACTCTCCAGTTAAAACCCATTCTCTAGCAAATGTAGCTTTTGATGAAGCCATTGTTGAGCTTGATACATTTA
GTGAGGAGTCATACAAGGACTGTACACTAATAACACAATTACTGAGAGACAACTAGACATTGTGGACATCAGCTTCCCAA
GAAGATGAAGCTGAAGCAGGA

ORF - retro_cpor_644 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.16 %
Parental protein coverage: 90.61 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalYDDMAACMKSVTEQGAELSNEERNLLSV-AYKNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIE
Y..MAA..KSV.EQG..LSNEERNLL.V...KNV.GA..SSW.VVSS.EQK.EGAE..QQMA.E.REK.E
RetrocopyYNAMAAHVKSVSEQGTGLSNEERNLLCV<SSKNVTGAYSSSWKVVSSTEQKMEGAETGQQMAQEHREKTE
ParentalTELRDICNDVLSLLE-KFLIPNASQAESK-VFYLKMKGDYYRY-LAEVAAGDDKKGIVDQSQQAYQE-AF
.ELR..CN.VLSLLE.K.L.P..........FYLK.KGDYY.Y.L..VAAGDD.KGIV.QSQQ.YQ...F
RetrocopyAELRLTCNNVLSLLE<KVLDPQCFTSREQ<AFYLKTKGDYYCY<LSGVAAGDDQKGIVGQSQQRYQK<VF
ParentalEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRD
EI..KEMQP.HPIRL.L.LN.S.FYYEILNSP.K..SLA..AFDEAI.ELDT.SEESYKD.TLI.QLLRD
RetrocopyEIRIKEMQPMHPIRLSLTLNYSMFYYEILNSPVKTHSLANVAFDEAIVELDTFSEESYKDCTLITQLLRD
ParentalNLTLWTSDTQGDEAEAG
N.TLWTS..Q.DEAEAG
RetrocopyN*TLWTSASQEDEAEAG

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 310 .76 RPM
SRP017611_kidney 0 .00 RPM 57 .89 RPM
SRP017611_liver 0 .00 RPM 21 .33 RPM
SRP040447_lung 0 .00 RPM 92 .13 RPM
SRP040447_skeletal_muscle 0 .00 RPM 17 .82 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_644 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_644 was not experimentally validated.

Retrocopy orthology:
Cavia porcellus 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.

Parental genes homology:
Parental genes homology involve 26 parental genes, and 99 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086942 retrocopies
Bos taurus ENSBTAG000000002364 retrocopies
Canis familiaris ENSCAFG000000005806 retrocopies
Choloepus hoffmanni ENSCHOG000000027989 retrocopies
Callithrix jacchus ENSCJAG000000158445 retrocopies
Cavia porcellus ENSCPOG000000080071 retrocopy
Cavia porcellus ENSCPOG000000113214 retrocopies
Cavia porcellus ENSCPOG00000020285 5 retrocopies
Dasypus novemcinctus ENSDNOG0000000167210 retrocopies
Ficedula albicollis ENSFALG000000058601 retrocopy
Felis catus ENSFCAG000000320174 retrocopies
Gallus gallus ENSGALG000000107251 retrocopy
Gorilla gorilla ENSGGOG000000221339 retrocopies
Loxodonta africana ENSLAFG000000049442 retrocopies
Myotis lucifugus ENSMLUG000000173233 retrocopies
Macaca mulatta ENSMMUG000000064897 retrocopies
Mus musculus ENSMUSG000000222853 retrocopies
Oryctolagus cuniculus ENSOCUG000000007342 retrocopies
Pongo abelii ENSPPYG000000187917 retrocopies
Pelodiscus sinensis ENSPSIG000000037031 retrocopy
Sarcophilus harrisii ENSSHAG000000126712 retrocopies
Sus scrofa ENSSSCG000000060622 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000238643 retrocopies
Taeniopygia guttata ENSTGUG000000120781 retrocopy
Tursiops truncatus ENSTTRG000000159064 retrocopies
Vicugna pacos ENSVPAG000000058651 retrocopy



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