RetrogeneDB ID:

retro_cpor_46

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_87:5129092..5130682(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000019576
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCPOG00000026318
Aliases:None
Description:Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:H0VVB1]


Retrocopy-Parental alignment summary:






>retro_cpor_46
ATGTCCACCAATGAGAATGCTAATTCACCAGCTGCCCGCCTGAACAGATTCAAGAACAAGGGGAAAGACAGCACCGAAAT
GAGGCGACGCCGAATAGAAGTTAATGTGGAGCTAAGGAAAGCTAAGAAGGATGACCAGATGCTGAAAAGGAGAAATGTAA
GCTCCTTTCCTGATGATGCTACTTCACCACTGCAGGAAAACCGCAACAACCAGGGCACTGTGAATTGGACTGTTGATGAC
ATTGTCAAAGGTATAAATAGCAATAATCTGGAAAACCAGCTCCAAGCTACTCAAGCTGCTAGGAAACTGCTTTCTCGTGA
AAAACAGCCCCCCATAGATCACATAATCCGGGCTGGTTTGATTCCAAAATTTGTGTCCTTCTTGGGCAGAACTGACTGTA
GTCCCATTCAGTTTGAGTCTGCTTGGGCGCTCACTAACATTGCTTCTGGGTCATCAGAACAGACCAAGGCTGTGGTGGAC
GGAGGTGCTATCCCAGCACTCATTTCTCTCTTGGCCTCTCCCCATGCCCACATCAGTGAACAGGCTGTCTGGGCTCTAGG
AAACATTGCAGGTGATGGTTCAGTTTTCCGAGACTTGGTTATCAAATATGGTGCAATTGACCCGCTCTTAGCTCTTCTTG
CAGTTCCTGATATGTCATCTTTAGCCGGTGGTTACTTACGTAATCTTACCTGGACACTTTCAAACCTTTGCCGCAACAAG
AATCCTGCACCCCCATTAGATGCTGTTGAGCAAATTCTTCCTACCTTGGTTCGTCTCCTACATCACAATGATCTTGAAGT
ATTAGCAGATACCTGCTGGGCTATTTCTTACCTTACAGATGGTCCAAATGAGCGCATTGAAATGGTTTTAAAAACTGGAG
TTGTGCCCCATCTGGTGAAGCTTCTAGGATCAAATGAATTATCCATTATGACTCCTGCGCTAAGAGCCATAGGGAATATT
GTTACTGGAACAGATGAACAGACTCAGATTGTAATAGATGCAGGAGCACTCGCTGTTTTTCCCAGCCTGCTTGTTCACCC
CAAAACTAATATTCAGAAGGAAGCTACCTGGACAATGTCAAACATCACAGCCGGCCGCCAGGACCAGATACAGCAAGTTG
TCAATCATGGATTAGTCCCGATCCTTGTCAGTGTTCTCTCTAAGGCAGACTTTAAGACACAAAAGGAAGCTGTGTGGGCT
GTGACCAACTACACCAGTGGTGGGACAGTTGAACAGATTGTTTACCTTGTTCATTGTGGGATGATAGAACCATTGATGAA
CCTCTTAACTGCCAAAGATACGAAAATCATTCTTGTTATTCTGGATGCCATTTCAAATATCTTCCAGGCTGCTGAGAAAT
TAGGTGAAACGGAGAAGCTTAGTATAATGATCGAAGAATGCGGAGGTTTGGACAAGATTGAAGCACTGCAGAACCATGAA
AACGAGTCTGTGTACAAGGCCTCCTTAAACTTGATTGAGAAGTACTTCTCAGTAGAGGAAGAAGAAGATCAAACTGTTGT
GCCAGAAACTACCTCTGAAGGCTATACTTTCCAAGTTCAGGACGGGGCTCCTGGTTCCTTTAACTTCTAG

ORF - retro_cpor_46 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSTNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
MSTNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
RetrocopyMSTNENANSPAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
ParentalQGTVNWTVDDIVKGINSNNLENQLQATQAARKLLSREKQPPIDHIIRAGLIPKFVSFLGRTDCSPIQFES
QGTVNWTVDDIVKGINSNNLENQLQATQAARKLLSREKQPPIDHIIRAGLIPKFVSFLGRTDCSPIQFES
RetrocopyQGTVNWTVDDIVKGINSNNLENQLQATQAARKLLSREKQPPIDHIIRAGLIPKFVSFLGRTDCSPIQFES
ParentalAWALTNIASGSSEQTKAVVDGGAIPALISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAIDPLL
AWALTNIASGSSEQTKAVVDGGAIPALISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAIDPLL
RetrocopyAWALTNIASGSSEQTKAVVDGGAIPALISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAIDPLL
ParentalALLAVPDMSSLAGGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDLEVLADTCWAISYLTD
ALLAVPDMSSLAGGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDLEVLADTCWAISYLTD
RetrocopyALLAVPDMSSLAGGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDLEVLADTCWAISYLTD
ParentalGPNERIEMVVKTGVVPHLVKLLGSNELSIMTPALRAIGNIVTGTDEQTQIVIDAGALAVFPSLLVHPKTN
GPNERIEMV.KTGVVPHLVKLLGSNELSIMTPALRAIGNIVTGTDEQTQIVIDAGALAVFPSLLVHPKTN
RetrocopyGPNERIEMVLKTGVVPHLVKLLGSNELSIMTPALRAIGNIVTGTDEQTQIVIDAGALAVFPSLLVHPKTN
ParentalIQKEATWTMSNITAGRQDQIQQVVNHGLVPILVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCG
IQKEATWTMSNITAGRQDQIQQVVNHGLVPILVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCG
RetrocopyIQKEATWTMSNITAGRQDQIQQVVNHGLVPILVSVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCG
ParentalIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLN
.IEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLN
RetrocopyMIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKASLN
ParentalLIEKYFSVEEEEDQTVVPETTSEGYTFQVQDGAPGSFNF
LIEKYFSVEEEEDQTVVPETTSEGYTFQVQDGAPGSFNF
RetrocopyLIEKYFSVEEEEDQTVVPETTSEGYTFQVQDGAPGSFNF

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 .35 RPM 8 .97 RPM
SRP017611_kidney 1 .05 RPM 11 .83 RPM
SRP017611_liver 0 .96 RPM 11 .10 RPM
SRP040447_lung 2 .57 RPM 34 .00 RPM
SRP040447_skeletal_muscle 0 .97 RPM 12 .32 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_46 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_46 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 70 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG00000026318 1 retrocopy
retro_cpor_46 ,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,




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