RetrogeneDB ID:

retro_cpor_1194

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_54:7676717..7677266(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1B
Ensembl ID:ENSCPOG00000008272
Aliases:None
Description:RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]


Retrocopy-Parental alignment summary:






>retro_cpor_1194
ATGCCTAAGTATAAGCCAGTTGTTCTTGGCTTAGGAGGCATTAGAAAGCCTGCTCCGCCTGTACAGTTTGTTCAAAGAAT
TTTTGTTGAAAAATATGAACCCAAGAGAGAAGATTCTTATAGAAAGTAAATTGAAGTAGATGTACAGCAGCATATGCTTG
AAATTGTGAATACTGCAAGAATGGAACAATTTATAGCAATGAGAGATTTGTACATGAAAAATGGAGAAGGCTTTGCTTTA
GTTTATTCCATCATAGCAGAGTCCACATTTGATGATCTACAAGATCTGAGAGAACAGTTTCTTCAGGTTAAAGACACTGA
GGATGTTCCAATGATTCTGGTTGGTAATAAATGTGGCTTGGGAGATGAAAAAGTTGTAGGAAAGGAACAAGGTCAAAATC
TAGCAAGACAGTGGAACAACTGTGCATTCTTAGAATCTGCAAAACAAAAAATATATGTTAATGAGATCTTTTGTGATCTA
GTGCAGCAAATTAAAGGAAAAACTTCAGTGCCTGGGAAGACCTGCAATAAGTCGTCATATCAACTGCTT

ORF - retro_cpor_1194 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.09 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDTAGTEQFTAMRDL
M..YK.VVLG.GG..K.A..VQFVQ.IFVEKY.P..EDSYRK..EVD.QQ.MLEI..TA..EQF.AMRDL
RetrocopyMPKYKPVVLGLGGIRKPAPPVQFVQRIFVEKYEPKREDSYRK*IEVDVQQHMLEIVNTARMEQFIAMRDL
ParentalYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQWNN
YMKNG.GFALVYSI.A.STF.DLQDLREQ.L.VKDT.DVPMILVGNKC.L.DE.VVGKEQGQNLARQWNN
RetrocopyYMKNGEGFALVYSIIAESTFDDLQDLREQFLQVKDTEDVPMILVGNKCGLGDEKVVGKEQGQNLARQWNN
ParentalCAFLESSAKSKINVNEIFYDLVRQINRKTPVPGKARKKSSCQLL
CAFLES.AK.KI.VNEIF.DLV.QI..KT.VPGK...KSS.QLL
RetrocopyCAFLES-AKQKIYVNEIFCDLVQQIKGKTSVPGKTCNKSSYQLL

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 17 .49 RPM
SRP017611_kidney 0 .00 RPM 21 .36 RPM
SRP017611_liver 0 .00 RPM 23 .55 RPM
SRP040447_lung 0 .00 RPM 50 .06 RPM
SRP040447_skeletal_muscle 0 .00 RPM 8 .67 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_1194 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_1194 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 30 parental genes, and 78 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086371 retrocopy
retro_amel_103,
Bos taurus ENSBTAG000000089673 retrocopies
retro_btau_1564, retro_btau_297, retro_btau_684,
Callithrix jacchus ENSCJAG000000072613 retrocopies
retro_cjac_1435, retro_cjac_2371, retro_cjac_607,
Cavia porcellus ENSCPOG00000008272 4 retrocopies
retro_cpor_1194 , retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus ENSDNOG0000001972418 retrocopies
retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Dipodomys ordii ENSDORG000000010861 retrocopy
retro_dord_521,
Erinaceus europaeus ENSEEUG000000100521 retrocopy
retro_eeur_327,
Echinops telfairi ENSETEG000000002421 retrocopy
retro_etel_11,
Homo sapiens ENSG000001273142 retrocopies
retro_hsap_3338, retro_hsap_4234,
Gorilla gorilla ENSGGOG000000256491 retrocopy
retro_ggor_2836,
Loxodonta africana ENSLAFG000000164601 retrocopy
retro_lafr_482,
Microcebus murinus ENSMICG000000131481 retrocopy
retro_mmur_116,
Myotis lucifugus ENSMLUG000000166062 retrocopies
retro_mluc_1126, retro_mluc_2211,
Macaca mulatta ENSMMUG000000114422 retrocopies
retro_mmul_1151, retro_mmul_1863,
Monodelphis domestica ENSMODG000000073235 retrocopies
retro_mdom_11, retro_mdom_1570, retro_mdom_1756, retro_mdom_1897, retro_mdom_429,
Mus musculus ENSMUSG000000526811 retrocopy
retro_mmus_1370,
Nomascus leucogenys ENSNLEG000000035732 retrocopies
retro_nleu_1034, retro_nleu_481,
Oryctolagus cuniculus ENSOCUG000000295525 retrocopies
retro_ocun_1132, retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii ENSOGAG000000057462 retrocopies
retro_ogar_2260, retro_ogar_272,
Procavia capensis ENSPCAG000000109771 retrocopy
retro_pcap_8,
Pongo abelii ENSPPYG000000047511 retrocopy
retro_pabe_3403,
Pan troglodytes ENSPTRG000000051973 retrocopies
retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus ENSRNOG000000070484 retrocopies
retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sarcophilus harrisii ENSSHAG000000114971 retrocopy
retro_shar_425,
Sus scrofa ENSSSCG000000211481 retrocopy
retro_sscr_1125,
Sus scrofa ENSSSCG000000300142 retrocopies
retro_sscr_435, retro_sscr_909,
Tupaia belangeri ENSTBEG000000133804 retrocopies
retro_tbel_2145, retro_tbel_4650, retro_tbel_4658, retro_tbel_613,
Tarsius syrichta ENSTSYG000000001921 retrocopy
retro_tsyr_910,
Tursiops truncatus ENSTTRG000000157122 retrocopies
retro_ttru_1105, retro_ttru_134,
Vicugna pacos ENSVPAG000000009312 retrocopies
retro_vpac_283, retro_vpac_408,


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