RetrogeneDB ID:

retro_cpor_1462

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_89:5320902..5321412(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CACYBP
Ensembl ID:ENSCPOG00000012682
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1462
CCAGAACTTCTTGACAGTGAAAAACCGGCTGTTATATCTGTTCCTATCAAACAGAATACCCTGTGAATGTCAGTCATTAT
GGGTAGGGCCAGCCTGATAAGTTTGTGAAAATCTACATTACTTTAACTGGAGTTCATCGAGTTCCTGCCGACAACACACA
GGTGGATTTCACGGAGAGGTCATTTGATCTTTTGGTAAAGAACCATTTAGGTTCTTTACCTATTTAAGGAACAATCTTCT
TGAAACCACCTCAGTGCAAGGCAGTTCAAAAAAAATTAAGACTGACACAGTTCTCATCTTGTGTAGAAAGAAAGCAGAAA
ACACTCAGTGGGAGAACGTCACTCAGGTTGAGAAAGAGTACAAAGAAAAACAAAAGCCACCTACGATGCTGAGACAGATC
CTAATGAGGGACTAACGAATGTTCTAAAGAGAATTTATGAAAATGGAGATGATAATATGAAGTGGACCACTATTAAAACC
TGGGACAAGAGAGAAGCAAACCAAAGGAGA

ORF - retro_cpor_1462 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.14 %
Parental protein coverage: 74.78 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPELHDSEKPAAVVAPIT-TGYTVKISNYGWDQSDKFVKIYITLTGVHQVPAENVQVYFTERSFDLLVKNL
PEL.DSEKPA....PI..T.Y.V..S.YG..Q.DKFVKIYITLTGVH.VPA.N.QV.FTERSFDLLVKN.
RetrocopyPELLDSEKPAVISVPIK<TEYPVNVSHYG*GQPDKFVKIYITLTGVHRVPADNTQVDFTERSFDLLVKNH
ParentalNGKSYSMIVNNLLKP-ISVEGSSKKIKTDTVLILCRKKAENVQWEYLTQVEKECKEKEKP-SYDAETDPS
.G.S........LKP..SV.GS....KTDTVLILCRKKAEN.QWE..TQVEKE.KEK.KP..YDAETDP.
RetrocopyLG-SLPI*GTIFLKP<TSVQGSXXXXKTDTVLILCRKKAENTQWENVTQVEKEYKEKQKP<TYDAETDPN
ParentalEGLMNVLKKIYEDGDDDMKRTINKAWVESREKQAK
EGL.NVLK.IYE.GDD.MK.T..K.W......Q..
RetrocopyEGLTNVLKRIYENGDDNMKWTTIKTWDKREANQRR

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 43 .89 RPM
SRP017611_kidney 0 .00 RPM 41 .98 RPM
SRP017611_liver 0 .00 RPM 36 .34 RPM
SRP040447_lung 0 .00 RPM 34 .43 RPM
SRP040447_skeletal_muscle 0 .00 RPM 35 .18 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1462 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1462 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 68 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000001704 retrocopies
Bos taurus ENSBTAG000000011071 retrocopy
Canis familiaris ENSCAFG000000290161 retrocopy
Callithrix jacchus ENSCJAG000000089894 retrocopies
Cavia porcellus ENSCPOG00000012682 7 retrocopies
Dasypus novemcinctus ENSDNOG000000156291 retrocopy
Dipodomys ordii ENSDORG000000018701 retrocopy
Erinaceus europaeus ENSEEUG000000149732 retrocopies
Echinops telfairi ENSETEG000000093313 retrocopies
Felis catus ENSFCAG000000085913 retrocopies
Homo sapiens ENSG000001161612 retrocopies
Gorilla gorilla ENSGGOG000000059622 retrocopies
Macropus eugenii ENSMEUG000000107255 retrocopies
Macaca mulatta ENSMMUG000000015711 retrocopy
Mustela putorius furoENSMPUG000000048133 retrocopies
Mus musculus ENSMUSG000000142264 retrocopies
Nomascus leucogenys ENSNLEG000000153573 retrocopies
Oryctolagus cuniculus ENSOCUG000000043583 retrocopies
Otolemur garnettii ENSOGAG000000053752 retrocopies
Ochotona princeps ENSOPRG000000003161 retrocopy
Procavia capensis ENSPCAG000000037423 retrocopies
Pongo abelii ENSPPYG000000004863 retrocopies
Pan troglodytes ENSPTRG000000017052 retrocopies
Rattus norvegicus ENSRNOG000000025722 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000108594 retrocopies
Tursiops truncatus ENSTTRG000000103991 retrocopy



Copyright © RetrogeneDB 2014-2017