RetrogeneDB ID:

retro_cpor_12

Retrocopy
location
Organism:Guinea Pig (Cavia porcellus)
Coordinates:scaffold_87:6749006..6749981(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCPOG00000005713
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:WDR5
Ensembl ID:ENSCPOG00000014790
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cpor_12
ATGGCGGCAGAGGAGCCCCGAGGCGCCTTCTCATCAGCCTGGCGGCACCAGGAAATGCCTACAAAACCGAACTATGCGCT
CAAACTTACTCTTGAGGGGCACACGGAAGCAGTGTCTTCAGTTAAGTTTAGTCCTGACGGGGAATGGCTAGCAAGTTCTT
CTGCTGATAAAGTAATTATAATTTGGGGAGCATATGATGGGAACTACGAGAAAACCCTATATGGCCACAACCTGGAAATA
TCAGACGTTGCCTGGTCATCAGATTCTAGTTGTCTTGTTTCCGCTTCAGATGATAAAACCCTGAAGATATGGGATGTGAG
ATCTGGAAAATGTTTGAAAACACTAAAGGGACACAATGATTATGTCTTTTGTTGTAATTTCAACCCTGCATCCACGCTAA
TCGTTTCAGGATCTTTTGATGAGAGCGTGAAAATATGGGAAGTGAAAACAGGAAAGTGCCTTAAGACTTTGACTGCTCAT
TCTGACCCAGTTTCTGCTGTTCATTTTAATAGCACGGGGTCCTTGATAGTGTCAGGTAGCTACGATGGCCTCTGTAGAAT
CTGGGATGCTGCCTCGGGTCAGTGTTTAAAAACACTTGCTGTTGATGACAATCTTCCTGTCTCTTTTGTAAAATTTTCTC
CAAATGGTAAATATATTCTCATTTCAACTTTGGACAGTACACTTAAACTGTGGGATTACAGCAGAGGCAGATGTTTGAAG
ACATACAGTGGTCATAAGAATGAGAAATACTGCATATTTTCCAATTTTTCAGTTACTGGTGGAAAGTGGATTGTGTCTGG
CTCGGAGGATAACCTGGTGTACATTTGGAGCATTCAGACTAAAGAGATTGTACAGAAATTACAAGGTCATACTGATGTTG
TGATTGCAGCAGCTTGTCATCCTACAGAAAACATCATCGCCTCAGCAGCACTGGAAAATGACAAAACAATTAAACTATGG
ATGAGTGACTACTAA

ORF - retro_cpor_12 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.66 %
Parental protein coverage: 93.71 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGI
SSA......P.KPNYALK.TL.GHT.AVSSVKFSP.GEWLASSSADK.I.IWGAYDG..EKT..GH.L.I
RetrocopySSAWRHQEMPTKPNYALKLTLEGHTEAVSSVKFSPDGEWLASSSADKVIIIWGAYDGNYEKTLYGHNLEI
ParentalSDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKT
SDVAWSSDS..LVSASDDKTLKIWDV.SGKCLKTLKGH..YVFCCNFNP.S.LIVSGSFDESV.IW.VKT
RetrocopySDVAWSSDSSCLVSASDDKTLKIWDVRSGKCLKTLKGHNDYVFCCNFNPASTLIVSGSFDESVKIWEVKT
ParentalGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYIL
GKCLKTL.AHSDPVSAVHFN..GSLIVS.SYDGLCRIWD.ASGQCLKTL..DDN.PVSFVKFSPNGKYIL
RetrocopyGKCLKTLTAHSDPVSAVHFNSTGSLIVSGSYDGLCRIWDAASGQCLKTLAVDDNLPVSFVKFSPNGKYIL
ParentalAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGH
..TLD.TLKLWDYS.G.CLKTY.GHKNEKYCIF.NFSVTGGKWIVSGSEDNLVYIW..QTKEIVQKLQGH
RetrocopyISTLDSTLKLWDYSRGRCLKTYSGHKNEKYCIFSNFSVTGGKWIVSGSEDNLVYIWSIQTKEIVQKLQGH
ParentalTDVVISTACHPTENIIASAALENDKTIKLWKSD
TDVVI..ACHPTENIIASAALENDKTIKLW.SD
RetrocopyTDVVIAAACHPTENIIASAALENDKTIKLWMSD

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 2 .07 RPM 18 .64 RPM
SRP017611_kidney 3 .98 RPM 23 .87 RPM
SRP017611_liver 3 .92 RPM 12 .32 RPM
SRP040447_lung 2 .98 RPM 27 .16 RPM
SRP040447_skeletal_muscle 1 .35 RPM 11 .88 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_12 retrocopy.

TSS - click to see more details

Cavia porcellus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cpor_12 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 28 parental genes, and 31 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111791 retrocopy
retro_amel_29,
Bos taurus ENSBTAG000000470311 retrocopy
retro_btau_299,
Canis familiaris ENSCAFG000000198301 retrocopy
retro_cfam_128,
Callithrix jacchus ENSCJAG000000101231 retrocopy
retro_cjac_1,
Cavia porcellus ENSCPOG000000062121 retrocopy
retro_cpor_819,
Cavia porcellus ENSCPOG000000107472 retrocopies
retro_cpor_1531, retro_cpor_548,
Cavia porcellus ENSCPOG00000014790 1 retrocopy
retro_cpor_12 ,
Dipodomys ordii ENSDORG000000150101 retrocopy
retro_dord_7,
Equus caballus ENSECAG000000173891 retrocopy
retro_ecab_82,
Echinops telfairi ENSETEG000000157311 retrocopy
retro_etel_15,
Felis catus ENSFCAG000000057121 retrocopy
retro_fcat_119,
Homo sapiens ENSG000001963631 retrocopy
retro_hsap_11,
Gorilla gorilla ENSGGOG000000049972 retrocopies
retro_ggor_171, retro_ggor_2023,
Loxodonta africana ENSLAFG000000111921 retrocopy
retro_lafr_55,
Microcebus murinus ENSMICG000000080851 retrocopy
retro_mmur_34,
Myotis lucifugus ENSMLUG000000022361 retrocopy
retro_mluc_11,
Macaca mulatta ENSMMUG000000141591 retrocopy
retro_mmul_190,
Mustela putorius furoENSMPUG000000121841 retrocopy
retro_mputfur_2,
Mus musculus ENSMUSG000000269171 retrocopy
retro_mmus_132,
Nomascus leucogenys ENSNLEG000000134721 retrocopy
retro_nleu_63,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000236532 retrocopies
retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus ENSPVAG000000016661 retrocopy
retro_pvam_112,
Rattus norvegicus ENSRNOG000000082121 retrocopy
retro_rnor_258,
Sus scrofa ENSSSCG000000249121 retrocopy
retro_sscr_1,
Ictidomys tridecemlineatus ENSSTOG000000158991 retrocopy
retro_itri_117,
Drosophila melanogaster FBgn00400661 retrocopy
retro_dmel_69,


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