RetrogeneDB ID:

retro_cpor_5

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_3:61109943..61110996(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000001179
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM185A
Ensembl ID:ENSCPOG00000003622
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_5
ATGAACCCCAGGGGGTTGTTCCAGGACTTCAACCCCAGTAAGTTCCTCATCTACGCCTGCCTTCTGCTTTTCTCCGTGTT
GCTGCCTCTGCGCTTGGACGGCGTCATCCAGTGGAGCTACTGGGCCGTGTTTGCCCCCATATGGCTATGGAAGCTCCTGG
TCGTCGCGGGGGCCTCGGTGGGTGCGGGCGTTTGGGCTCGCAACCCTCGCTACCGCACCGAGGGGGAGGCCGGCGTGGAG
TTCAAAGCCATGCTGATCGCCGTGGGCATCCACTTGCTGCTGCTCATGTTCGAAGTACTGGTCTGTGACCGGGTGGAGAG
GGGCACCCATTTCTGGCTGCTGGTCTTCATGCCTCTCTTCTTCGTCTCCCCCGTGTCTGTGGCCGCTTGTGTCTGGGGCT
TTCGACACGACAGGTCGCTGGAGCTGGAGATCCTGTGCTCCGTCAATATCCTGCAGTTCATCTTCATTGCCTTGAGGCTG
GACAGGATTATCCACTGGCCCTGGCTGGTGGTGTTCGTGCCGCTGTGGATCCTCATGTCCTTCCTTTGTCTGGTTGTCCT
CTATTACATCGTCTGGTCCCTCCTGTTTCTGAGGTCCCTGGACGTGGTCGCAGAGCAGCGAAGAACCCACGTGACCATGG
CCATCAGCTGGATAACGATTGTTGTGCCTCTGCTCACTTTTGAGGTCCTGCTGGTTCACAGATTGGATGGCCACAATACC
TTCTCTTACATCTCCATATTTGTCCCCCTTTGGCTGTCACTAGTAACTTTGATGGCCACAACTTTTAGGCGAAAAGGAGG
CAATCATTGGTGGTTTGGCATTCGCAGAGATTTCTGTCAGTTTCTGCTCGAAATTTTTCCATTTTTAAGAGAATATGGGA
ACATTTCCTATGATCTCCAACATGAAGATAGTGAAGACCCTGAAGAAACTGCCGGTCCAGAAGCTCCAAAAATCCCCCCA
ATGTTTGGAAAGAAGGCCAGGGTAGTTGTAACACAGAGCCCTGGAAAATACGTTCCCCCACCTCCTAAGTTAAATATTGA
TATGCCAGACTAG

ORF - retro_cpor_5 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.68 %
Parental protein coverage: 97.43 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFSPSKFLIYACLLLFSVLLALRLDGIIQWSYWAVFAPIWLWKLMVIVGASVGTGVWARNPQYRAEGETCV
F.PSKFLIYACLLLFSVLL.LRLDG.IQWSYWAVFAPIWLWKL.V..GASVG.GVWARNP.YR.EGE..V
RetrocopyFNPSKFLIYACLLLFSVLLPLRLDGVIQWSYWAVFAPIWLWKLLVVAGASVGAGVWARNPRYRTEGEAGV
ParentalEFKAMLIAVGIHLLLLMFEVLVCDRIERGSHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
EFKAMLIAVGIHLLLLMFEVLVCDR.ERG.HFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
RetrocopyEFKAMLIAVGIHLLLLMFEVLVCDRVERGTHFWLLVFMPLFFVSPVSVAACVWGFRHDRSLELEILCSVN
ParentalILQFIFIALRLDKIIHWPWLVVCVPLWILMSFLCLVVLYYIVWSVLFLRSMDVIAEQRRTHITMALSWMT
ILQFIFIALRLD.IIHWPWLVV.VPLWILMSFLCLVVLYYIVWS.LFLRS.DV.AEQRRTH.TMA.SW.T
RetrocopyILQFIFIALRLDRIIHWPWLVVFVPLWILMSFLCLVVLYYIVWSLLFLRSLDVVAEQRRTHVTMAISWIT
ParentalIVVPLLTFEILLVHKLDGHNAFSCIPIFVPLWLSLITLMATTFGQKGGNHWWFGIRKDFCQFLLEIFPFL
IVVPLLTFE.LLVH.LDGHN.FS.I.IFVPLWLSL.TLMATTF..KGGNHWWFGIR.DFCQFLLEIFPFL
RetrocopyIVVPLLTFEVLLVHRLDGHNTFSYISIFVPLWLSLVTLMATTFRRKGGNHWWFGIRRDFCQFLLEIFPFL
ParentalREYGNISYDLHHEDNEETEETPVPEPPKIAPMFRKKARVVITQSPGKYVLPPPKLNIEMPD
REYGNISYDL.HED.E..EET..PE.PKI.PMF.KKARVV.TQSPGKYV.PPPKLNI.MPD
RetrocopyREYGNISYDLQHEDSEDPEETAGPEAPKIPPMFGKKARVVVTQSPGKYVPPPPKLNIDMPD

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 11 .27 RPM 9 .49 RPM
SRP017611_kidney 11 .20 RPM 8 .90 RPM
SRP017611_liver 4 .35 RPM 2 .92 RPM
SRP040447_lung 17 .38 RPM 10 .06 RPM
SRP040447_skeletal_muscle 7 .11 RPM 8 .93 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_5 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_5 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 22 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000086371 retrocopy
retro_acar_65,
Ailuropoda melanoleuca ENSAMEG000000093511 retrocopy
retro_amel_8,
Cavia porcellus ENSCPOG00000003622 1 retrocopy
retro_cpor_5 ,
Dasypus novemcinctus ENSDNOG000000118641 retrocopy
retro_dnov_2451,
Dipodomys ordii ENSDORG000000150271 retrocopy
retro_dord_67,
Equus caballus ENSECAG000000093991 retrocopy
retro_ecab_426,
Homo sapiens ENSG000001559841 retrocopy
retro_hsap_104,
Gorilla gorilla ENSGGOG000000242681 retrocopy
retro_ggor_189,
Loxodonta africana ENSLAFG000000030441 retrocopy
retro_lafr_898,
Microcebus murinus ENSMICG000000046391 retrocopy
retro_mmur_106,
Myotis lucifugus ENSMLUG000000013191 retrocopy
retro_mluc_2075,
Macaca mulatta ENSMMUG000000028881 retrocopy
retro_mmul_310,
Mustela putorius furoENSMPUG000000118961 retrocopy
retro_mputfur_46,
Mus musculus ENSMUSG000000731391 retrocopy
retro_mmus_358,
Nomascus leucogenys ENSNLEG000000134871 retrocopy
retro_nleu_2723,
Otolemur garnettii ENSOGAG000000164141 retrocopy
retro_ogar_88,
Pongo abelii ENSPPYG000000208091 retrocopy
retro_pabe_118,
Pteropus vampyrus ENSPVAG000000138221 retrocopy
retro_pvam_30,
Rattus norvegicus ENSRNOG000000110471 retrocopy
retro_rnor_6,
Sus scrofa ENSSSCG000000127391 retrocopy
retro_sscr_494,
Ictidomys tridecemlineatus ENSSTOG000000144841 retrocopy
retro_itri_8,
Tursiops truncatus ENSTTRG000000006431 retrocopy
retro_ttru_868,


Copyright © RetrogeneDB 2014-2017