RetrogeneDB ID:

retro_cpor_72

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_53:4661539..4663237(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000026487
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:KIF2A
Ensembl ID:ENSCPOG00000009393
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_72
ATGGCCAGCCAGACCTGCCTCCCTCTCGCCCCACGCCTCTGCCCTCTTAAACCTCTGAAGCCACACTGTGGAGACATCCA
GGCGGGAATTTGTGTGGTGATCGAGCGCAGCGACAACAGGATCCACCTGGCTGTGGTCACAGAGATCAACAGAGAAAACT
CTTGGGTCACAGTAGAATGGGTCGAGAAAGGAGTCAAGAAAGGTAAGAAGATTAATCTGGAGAACATCTTTCTGCTGAAT
CCAGCTCTGGCCTCCGCTGAATACCCCAAACCAATCAAGCCGTTGCCCCCTTTGTGTCTAGCAACCTCTCCAGCCATCGG
AGACCAGTGGGCAACCCCACAGTGGATGACCATGGCCCCCCAGAAAAGCGAAACACCGTCAGGAGACAGCCCAGCTGTGG
GCGTCCCCAGCCATCCCTGTCTGTTGAGGCAGAGAAAATCTCCTTGTCTGCGAGAAATTGAAAAACTGCAGAAGCAGCGA
GAAAAGCGCAGGCAGCTGCAACTGCAGATGCGATCCAGACGCGCATTAGAGGTCAACACCAGACACCCCAACCACGAGGT
CAGGCGCATGATAGAAGAGTGTCGCAAGGGCCTGGACAGCAGCAAGATTCCCACGCCTGGCCTGGAGCTCCCTGAACACC
AACGGATCTGTGTCTGCGTGAGGAAGAGGCCTCTCAACCAGCGGGAAACCACCATGAAGGACCTGGACATCATCACTATC
CTCTCGGGCAGCATGGTCATGGTGCATGAGTCCAAGCAAAAGCTGGACCTCACTCGCTATCTGGAGAACCAGACTTTCTG
TTTCGACCATGCCTTTGATGATACGGCGTCCAACGAGTTAGTGTACCAGTTCACCGCCCAGCCTCTGGTGGAGTCTATTT
TCCGCAAGGGCATGGCCACCTGCTTTGCCTACGGACAGACTGGCAGTGGGAAGACGCACACCATGGGCGGAGCCTTTTCA
GGAAGGGCCCAAGACTGTTCTAAAGGTATCTACGGCCTGGTGGCTCAGGATGTCTTTCTCCTGCTCAACAGCTCCACTTA
CAAGCAACTAGATCTCAAAGTCTATGGGACCTTTTTTGAGATTTATGGTGGCAAAGTGTATGATTTGTTGAACTGGAAGA
AAAAACTGCAAATTCTTGAAGATGGCAATCAGCAAATCCAAGTGGTCGGCCTGCGGGAAAAAGAGGTGCATTGTACGGAG
GAAGTGATGAACCTCGTGGAACTAGGCAACAGCTGCCGGACTTCCGGGCAGACCTCCGTTAATGTGCACTCATCCCGGAG
TCACGCAGTGTTTCAGATCACGTTGAAGTCCAGAGGAAAATTGCACGGCAAATTTTCCCTTATAGACTTAGCTGGAAATG
AAAGGGGAGCGGATACAGCCAAGGCCAACCGGAAGAGGCAGCTGGAAGGGGCAGAGATTAATAAGAGTCTCCTTGCCCTC
AAAGAATGTATCAGAGCTTTGGGTCAGAATAAGTCGCACACACCATTCAGAGCCAGCAAACTCACGCAAGTGCTTCGGGA
TTCCTTCATCGGTCAGAACTCCTCCACTTGCATGATTGCTACTATCTCGCCGGGGATGACCTCTTGTGAAAACACCCTCA
ACACTTTAAGATATGCAAATAGAGTAAAAGAATTAGCTCCAGAGGTAAGGCACTACCATCATTGCCTCTCAAAAATTAGA
CAGGAGGCACCACAGATT

ORF - retro_cpor_72 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.39 %
Parental protein coverage: 56.66 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalRRKSNCVKEVEKLQEKREKRRLQQQELREKRAQDVDATNPNYEIMCMIRDFRGSLDYRPLTTAD-PIDEH
.RKS.C..E.EKLQ..REKRR..Q...R..RA..V....PN.E...MI...R..LD.....T......EH
RetrocopyQRKSPCLREIEKLQKQREKRRQLQLQMRSRRALEVNTRHPNHEVRRMIEECRKGLDSSKIPTPGLELPEH
Parental-RICVCVRKRPLNKKETQMKDLDVITIPSKDVVMVHEPKQKVDLTRYLENQTFRFDYAFDDSAPNEMVYR
.RICVCVRKRPLN..ET.MKDLD.ITI.S...VMVHE.KQK.DLTRYLENQTF.FD.AFDD.A.NE.VY.
RetrocopyQRICVCVRKRPLNQRETTMKDLDIITILSGSMVMVHESKQKLDLTRYLENQTFCFDHAFDDTASNELVYQ
ParentalFTARPLVETIFERGMATCFAYGQTGSGKTHTMGGDFSGKNQDCSKGIYALAARDVFLMLKKPNYKKLELQ
FTA.PLVE.IF..GMATCFAYGQTGSGKTHTMGG.FSG..QDCSKGIY.L.A.DVFL.L....YK.L.L.
RetrocopyFTAQPLVESIFRKGMATCFAYGQTGSGKTHTMGGAFSGRAQDCSKGIYGLVAQDVFLLLNSSTYKQLDLK
ParentalVYATFFEIYSGKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLIDIGNSCRTSGQTSANAH
VY.TFFEIY.GKV.DLLN.K.KL..LEDG.QQ.QVVGL.E.EV.C.E.V..L...GNSCRTSGQTS.N.H
RetrocopyVYGTFFEIYGGKVYDLLNWKKKLQILEDGNQQIQVVGLREKEVHCTEEVMNLVELGNSCRTSGQTSVNVH
ParentalSSRSHAVFQIILRRKGKLHGKFSLIDLAGNERGADTSSADRQTRLEGAEINKSLLALKECIRALGRNKPH
SSRSHAVFQI.L...GKLHGKFSLIDLAGNERGADT..A.R...LEGAEINKSLLALKECIRALG.NK.H
RetrocopySSRSHAVFQITLKSRGKLHGKFSLIDLAGNERGADTAKANRKRQLEGAEINKSLLALKECIRALGQNKSH
ParentalTPFRASKLTQVLRDSFIGENSRTCMIATISPGMASCENTLNTLRYANRVKEL
TPFRASKLTQVLRDSFIG.NS.TCMIATISPGM.SCENTLNTLRYANRVKEL
RetrocopyTPFRASKLTQVLRDSFIGQNSSTCMIATISPGMTSCENTLNTLRYANRVKEL

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 64 .94 RPM
SRP017611_kidney 0 .00 RPM 13 .19 RPM
SRP017611_liver 0 .00 RPM 11 .67 RPM
SRP040447_lung 0 .00 RPM 18 .89 RPM
SRP040447_skeletal_muscle 0 .00 RPM 6 .69 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_72 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_72 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 24 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Anas platyrhynchos ENSAPLG000000095191 retrocopy
retro_apla_3,
Bos taurus ENSBTAG000000150221 retrocopy
retro_btau_180,
Choloepus hoffmanni ENSCHOG000000078881 retrocopy
retro_chof_1348,
Cavia porcellus ENSCPOG00000009393 1 retrocopy
retro_cpor_72 ,
Dipodomys ordii ENSDORG000000063351 retrocopy
retro_dord_763,
Equus caballus ENSECAG000000198101 retrocopy
retro_ecab_32,
Homo sapiens ENSG000000687961 retrocopy
retro_hsap_69,
Gorilla gorilla ENSGGOG000000047741 retrocopy
retro_ggor_68,
Macaca mulatta ENSMMUG000000003991 retrocopy
retro_mmul_145,
Monodelphis domestica ENSMODG000000196051 retrocopy
retro_mdom_242,
Mus musculus ENSMUSG000000216931 retrocopy
retro_mmus_68,
Nomascus leucogenys ENSNLEG000000028651 retrocopy
retro_nleu_2329,
Oryctolagus cuniculus ENSOCUG000000104661 retrocopy
retro_ocun_156,
Otolemur garnettii ENSOGAG000000005275 retrocopies
retro_ogar_126, retro_ogar_3166, retro_ogar_3498, retro_ogar_3501, retro_ogar_672,
Ochotona princeps ENSOPRG000000117681 retrocopy
retro_opri_815,
Procavia capensis ENSPCAG000000050891 retrocopy
retro_pcap_22,
Rattus norvegicus ENSRNOG000000140002 retrocopies
retro_rnor_1284, retro_rnor_47,
Sorex araneus ENSSARG000000077681 retrocopy
retro_sara_457,
Sarcophilus harrisii ENSSHAG000000019501 retrocopy
retro_shar_30,
Ictidomys tridecemlineatus ENSSTOG000000127101 retrocopy
retro_itri_40,
Tupaia belangeri ENSTBEG000000093961 retrocopy
retro_tbel_761,
Tarsius syrichta ENSTSYG000000021151 retrocopy
retro_tsyr_1791,
Vicugna pacos ENSVPAG000000088641 retrocopy
retro_vpac_572,
Drosophila melanogaster FBgn00302682 retrocopies
retro_dmel_1, retro_dmel_2,


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