RetrogeneDB ID:

retro_cpor_1275

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_63:3195548..3195983(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSCPOG00000001452
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_1275
AAGCGCAAAAAAGAAGCTCCTGCTCCTGCCAAAGCTGAGGCCAAAGAAAAGCTTTGAAGGTCAAAAACACTGAGCTGAAG
GCACCCAGTCACGAAAAGAAGATCCCCAAGTCACCCGCCTTCCACCTTCCCAAGACACTGCAGCCCAAATGTCCTCAGAG
GAGCACTCCCAGGAGAACCAAGCTGGATCCAGACACCATCATCAAGTTCTCCTGACCACGGCTTGGCCACAAAGAAGCCA
GAGGACAAAACACTGGTGTTCATGGTGGGTGCCAAGGCCATTGAGCCCCAGGTGGGACAAGCCCTTAAGAAGCTCGGTGA
CATCACTATGATCAAGGTCGGTACCCTCCCCAGGTCTGAGGCTGAGGAGAAGGCATGTGTTTATTTGGCTTCTGATTTTG
GTGCTTTGGGTGTTGCCAGGGCAATTTGGATCATC

ORF - retro_cpor_1275 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.05 %
Parental protein coverage: 98.08 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKAKKEAPAPPKAEAK-AKALKAKKAVLKGIHSHKKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLD
K.KKEAPAP.KAEAK..KALK.K...LK...SH..KKI..SP.F..PKTL....QPK.P..S.PRR.KLD
RetrocopyKRKKEAPAPAKAEAK<RKALKVKNTELKA-PSH-EKKIPKSPAFHLPKTL----QPKCPQRSTPRRTKLD
ParentalHYAIIKFP-LTTE-SAMKKIEDNNTLVFIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRL
...IIKF..LTT...A.KK.ED..TLVF.V..KA...Q..QA.KKL.DI...KV.TL.R...E.KA.V.L
RetrocopyPDTIIKFS<LTTA<LATKKPED-KTLVFMVGAKAIEPQVGQALKKLGDITMIKVGTLPRSEAEEKACVYL
ParentalAPDYDALDVANKIGII
A.D..AL.VA..I.II
RetrocopyASDFGALGVARAIWII

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 156 .96 RPM
SRP017611_kidney 0 .00 RPM 251 .77 RPM
SRP017611_liver 0 .00 RPM 164 .53 RPM
SRP040447_lung 0 .00 RPM 302 .47 RPM
SRP040447_skeletal_muscle 0 .01 RPM 269 .76 RPM
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1275 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1275 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 11 parental genes, and 254 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000053112 retrocopies
Cavia porcellus ENSCPOG00000001452 6 retrocopies
Dasypus novemcinctus ENSDNOG0000001948765 retrocopies
Equus caballus ENSECAG000000089281 retrocopy
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Procavia capensis ENSPCAG0000001700230 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies



Copyright © RetrogeneDB 2014-2017