RetrogeneDB ID:

retro_cpor_1400

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_8:31378315..31378613(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000004543
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1400
TACCCAATAAGGTCTATGGGTATTCACTTCCCCAGCAACATTCTTATTCTGGACAGTGGGTCTCTTGTCAAAAACCAGAG
TTTCTTGGATGAAAAATGACATCCGTCTGGTTTGGGTAAGGGCAGGTATTGCTTGTTCGGTATTTCAAGCCCAGAAAAAA
GAATTAATCCTTGAAAAGAATGATATTGAACTTACTTTAAAGTCGGCTACTTTGACTCAGTAAGCCATAACAATTAAAAA
CAAAGATATCAGAAAATTTTTGGATGGTATCTATGTTTCTGAAAAGGGAACAATTCAA

ORF - retro_cpor_1400 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.71 %
Parental protein coverage: 52.06 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYKMRSVYAHFPINVVIQENGSLVEIRNFLGEK-YIRRVRMRAVGVACSVSQAQKDELILEGNDIELVSNS
Y..RS...HFP.N..I...GSLV....FL.EK..IR.V..RA.G.ACSV.QAQK.ELILE.NDIEL...S
RetrocopyYPIRSMGIHFPSNILILDSGSLVKNQSFLDEK>DIRLVWVRA-GIACSVFQAQKKELILEKNDIELTLKS
ParentalVAALIQQATTVKNKDIRKFLDGIYVSEKGTVQ
.A.L.Q.A.T.KNKDIRKFLDGIYVSEKGT.Q
Retrocopy-ATLTQ*AITIKNKDIRKFLDGIYVSEKGTIQ

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 84 .20 RPM
SRP017611_kidney 0 .00 RPM 197 .34 RPM
SRP017611_liver 0 .00 RPM 143 .12 RPM
SRP040447_lung 0 .00 RPM 176 .34 RPM
SRP040447_skeletal_muscle 0 .00 RPM 206 .16 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1400 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1400 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 16 parental genes, and 225 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000073171 retrocopy
Cavia porcellus ENSCPOG00000004543 15 retrocopies
Danio rerio ENSDARG000000373501 retrocopy
Dasypus novemcinctus ENSDNOG0000000741118 retrocopies
Dipodomys ordii ENSDORG000000010886 retrocopies
Erinaceus europaeus ENSEEUG0000000439439 retrocopies
Gadus morhua ENSGMOG000000010021 retrocopy
Macropus eugenii ENSMEUG000000167228 retrocopies
Myotis lucifugus ENSMLUG0000000459734 retrocopies
Monodelphis domestica ENSMODG000000205537 retrocopies
Mus musculus ENSMUSG000000472152 retrocopies
Otolemur garnettii ENSOGAG0000000493520 retrocopies
Pteropus vampyrus ENSPVAG0000000091949 retrocopies
Rattus norvegicus ENSRNOG000000267163 retrocopies
Sarcophilus harrisii ENSSHAG000000049188 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000207713 retrocopies



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