RetrogeneDB ID:

retro_cpor_156

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_0:46302866..46303340(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2I
Ensembl ID:ENSCPOG00000010431
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_156
TTGTCTGGGATCACCCTCAGCAGACTCACCCAAGAGAGCAAAGCTTGAAGGAAAGACCACCCATTTGGCTTTGTGGCTGT
CCCTGCCAAGAATCCCGATGGCACAGTGAACCTGATGAACAGGGGGGTGCACCATCCCAGGGAAGAAGGAGATTCCCAGG
GAAGGAGGCTTATTCAACCTGCAGATGCTCTCAAAGGTGATTATCCATCCTCACCACCAAAATGTAAATTTTAGCTGCCA
CTCTTCCACCTGAATGTGTACCCCTCGGACACAGTGTGCCTGTCCATCCTGGAGGAAGACAAAAACTGGAGGCCAGCCAT
CATGATCAAACAGATCTTACTAGGACTACAGGAACTTCTAAATGAACCAGACATCCAAGACCCAGTTCAAGCAGAGGCCT
GCATTATCTACTGCCAAAACAGAGTGGAATATGAGAAAAGGGTTTGAGCACAAGCCAAGAAGTTTGCACCCTCG

ORF - retro_cpor_156 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.62 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMSGIALSRLAQERKAWRKDHPFGFVAVPTKNPDGTMNLMN-WECAIPGKKGTPWEGGLFKLRML-FKDDY
.SGI.LSRL.QE.KA.RKDHPFGFVAVP.KNPDGT.NLMN...C.IPGKK..P.EGGLF.L.ML..K.DY
RetrocopyLSGITLSRLTQESKA*RKDHPFGFVAVPAKNPDGTVNLMN>GGCTIPGKKEIPREGGLFNLQML<LKGDY
ParentalPSSPPKCKFEPPLFHPNVYPSGTVCLSILEEDKDWRPAITIKQILLGIQELLNEPNIQDPAQAEAYTIYC
PSSPPKCKF..PLFH.NVYPS.TVCLSILEEDK.WRPAI.IKQILLG.QELLNEP.IQDP.QAEA..IYC
RetrocopyPSSPPKCKF*LPLFHLNVYPSDTVCLSILEEDKNWRPAIMIKQILLGLQELLNEPDIQDPVQAEACIIYC
ParentalQNRVEYEKRVRAQAKKFAPS
QNRVEYEKRV.AQAKKFAPS
RetrocopyQNRVEYEKRV*AQAKKFAPS

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






RNA-Seq - click to see more details

(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 26 .69 RPM
SRP017611_kidney 0 .00 RPM 24 .60 RPM
SRP017611_liver 0 .00 RPM 15 .41 RPM
SRP040447_lung 0 .00 RPM 37 .10 RPM
SRP040447_skeletal_muscle 0 .00 RPM 17 .44 RPM

ChIP-Seq - click to see more details

Cavia porcellus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cpor_156 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_156 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 18 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000077211 retrocopy
retro_amel_1843,
Bos taurus ENSBTAG000000388661 retrocopy
retro_btau_1470,
Canis familiaris ENSCAFG000000314494 retrocopies
retro_cfam_1363, retro_cfam_1991, retro_cfam_2090, retro_cfam_541,
Callithrix jacchus ENSCJAG000000132491 retrocopy
retro_cjac_2914,
Cavia porcellus ENSCPOG00000010431 1 retrocopy
retro_cpor_156 ,
Equus caballus ENSECAG000000158311 retrocopy
retro_ecab_350,
Felis catus ENSFCAG000000272912 retrocopies
retro_fcat_1994, retro_fcat_873,
Loxodonta africana ENSLAFG000000183181 retrocopy
retro_lafr_541,
Myotis lucifugus ENSMLUG000000082292 retrocopies
retro_mluc_1112, retro_mluc_1327,
Macaca mulatta ENSMMUG000000036541 retrocopy
retro_mmul_981,
Mustela putorius furoENSMPUG000000157631 retrocopy
retro_mputfur_1234,
Mus musculus ENSMUSG000000151204 retrocopies
retro_mmus_1341, retro_mmus_1997, retro_mmus_3182, retro_mmus_3419,
Nomascus leucogenys ENSNLEG000000085251 retrocopy
retro_nleu_1298,
Otolemur garnettii ENSOGAG000000014284 retrocopies
retro_ogar_2367, retro_ogar_2731, retro_ogar_548, retro_ogar_641,
Rattus norvegicus ENSRNOG0000001790711 retrocopies
retro_rnor_1051, retro_rnor_1448, retro_rnor_1764, retro_rnor_1913, retro_rnor_2036, retro_rnor_2147, retro_rnor_2301, retro_rnor_2423, retro_rnor_2927, retro_rnor_708, retro_rnor_832,
Sarcophilus harrisii ENSSHAG000000070341 retrocopy
retro_shar_218,
Sus scrofa ENSSSCG000000215601 retrocopy
retro_sscr_319,
Ictidomys tridecemlineatus ENSSTOG000000102333 retrocopies
retro_itri_1341, retro_itri_1459, retro_itri_1601,


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