RetrogeneDB ID:

retro_cpor_123

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_122:736232..736946(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000000975
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:SPIN1
Ensembl ID:ENSCPOG00000000743
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_123
GGCGTGTCTGCATACCTGATGAAGAAAAGGCACACCCACAGGAAGCAGCGGCGCAAGCCCACTTTCCTCACTTGTAGGAA
CATAGTGGGCTGTCGCATTCAACACGGCTGGAAAGAAGGCAATGAGCCGGTGGAGCAGTGGAAGGGCACCGTACTCGAAC
AGGTTTCTGTGAAGCCCACACTCTACATCATTAAATATGATGGCAAAGATAGTGTGTATGGATTAGAACTTCACCGAGAT
AAAAGAGTTTTAGCGCTGGAGATTCTTCCTGAGAGAGTGCCAGCTCCTCGTATTGATTCACGCTTGGCAGATTCCTTGAT
TGGGAAAGCAGTGGGGCATGTGTTTGAAGGTGAGCACGGTACAAAAGATGAATGGAAGGGTATGGTACTGGCGCGAGCAC
CCGTGATGGATACTTGGTTTTATATCACCTATGAGAAAGATCCAGTCCTATATATGTACACCTTGCTGGATGACTACAAA
GATGGTGACCTTCGTATCATCCCAGATTCCAGCTACTATTTTCCTACAGCAGAACGGGAGCCTGGAGAAGTGATCGACAG
CCTCGTGGGCAAGCAGGTGGAGCACGCCAAAGATGATGGGTCCAAGAGAACTGGCATTTTCATTCATCAAGTGGTGGCCA
AGCCATCTGTTTACTTTATTAAGTTTGATGACGATATTCACATTTATGTCTATGGTTTGGTGAGAACTCCGTAA

ORF - retro_cpor_123 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.93 %
Parental protein coverage: 99.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRKHRSSVGPSKPVSQPRRNIVGCRIQHGWREGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELN
..H.......KP.....RNIVGCRIQHGW.EGN.PV.QWKGTVL.QV.V.P.LY.IKYDG.D.VYGLEL.
RetrocopyKRHTHRKQRRKPTFLTCRNIVGCRIQHGWKEGNEPVEQWKGTVLEQVSVKPTLYIIKYDGKDSVYGLELH
ParentalKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKD
.D.RV.ALE.LP.RV...RI.D..LAD..IGKAV.H.FE.E.G.KDEW.GMVLARAPVM.TWFYITYEKD
RetrocopyRDKRVLALEILPERVPAPRI-DSRLADSLIGKAVGHVFEGEHGTKDEWKGMVLARAPVMDTWFYITYEKD
ParentalPVLYMYQLLDDYKEGDLRIMPDSN-DSPPAEREPGEVVDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSV
PVLYMY.LLDDYK.GDLRI.PDS....P.AEREPGEV.DSLVGKQVE.AK.DGSKRTG..IHQV.AKPSV
RetrocopyPVLYMYTLLDDYKDGDLRIIPDSSYYFPTAEREPGEVIDSLVGKQVEHAKDDGSKRTGIFIHQVVAKPSV
ParentalYFIKFDDDFHIYVYDLVKT
YFIKFDDD.HIYVY.LV.T
RetrocopyYFIKFDDDIHIYVYGLVRT

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 .58 RPM 33 .53 RPM
SRP017611_kidney 1 .67 RPM 9 .42 RPM
SRP017611_liver 0 .09 RPM 5 .92 RPM
SRP040447_lung 1 .01 RPM 14 .10 RPM
SRP040447_skeletal_muscle 0 .30 RPM 3 .61 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_123 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_123 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 23 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000033014 retrocopies
retro_amel_1831, retro_amel_1879, retro_amel_38, retro_amel_41,
Bos taurus ENSBTAG000000030444 retrocopies
retro_btau_1678, retro_btau_1841, retro_btau_187, retro_btau_553,
Canis familiaris ENSCAFG000000022083 retrocopies
retro_cfam_153, retro_cfam_2095, retro_cfam_59,
Choloepus hoffmanni ENSCHOG000000069832 retrocopies
retro_chof_1343, retro_chof_1852,
Callithrix jacchus ENSCJAG000000174521 retrocopy
retro_cjac_227,
Cavia porcellus ENSCPOG00000000743 1 retrocopy
retro_cpor_123 ,
Echinops telfairi ENSETEG000000137191 retrocopy
retro_etel_28,
Felis catus ENSFCAG000000071972 retrocopies
retro_fcat_32, retro_fcat_70,
Homo sapiens ENSG000001067231 retrocopy
retro_hsap_64,
Loxodonta africana ENSLAFG000000274972 retrocopies
retro_lafr_18, retro_lafr_58,
Microcebus murinus ENSMICG000000145101 retrocopy
retro_mmur_8,
Myotis lucifugus ENSMLUG000000085162 retrocopies
retro_mluc_132, retro_mluc_1626,
Mustela putorius furoENSMPUG000000085851 retrocopy
retro_mputfur_139,
Mus musculus ENSMUSG000000213953 retrocopies
retro_mmus_112, retro_mmus_16, retro_mmus_3351,
Oryctolagus cuniculus ENSOCUG000000118801 retrocopy
retro_ocun_63,
Otolemur garnettii ENSOGAG000000021662 retrocopies
retro_ogar_2327, retro_ogar_9,
Procavia capensis ENSPCAG000000158001 retrocopy
retro_pcap_14,
Pongo abelii ENSPPYG000000193551 retrocopy
retro_pabe_33,
Pan troglodytes ENSPTRG000000210882 retrocopies
retro_ptro_116, retro_ptro_95,
Pteropus vampyrus ENSPVAG000000133913 retrocopies
retro_pvam_2, retro_pvam_22, retro_pvam_858,
Rattus norvegicus ENSRNOG000000111194 retrocopies
retro_rnor_1483, retro_rnor_1531, retro_rnor_281, retro_rnor_2818,
Ictidomys tridecemlineatus ENSSTOG000000291071 retrocopy
retro_itri_136,
Tursiops truncatus ENSTTRG000000056026 retrocopies
retro_ttru_1061, retro_ttru_13, retro_ttru_1452, retro_ttru_1506, retro_ttru_1669, retro_ttru_1698,


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