RetrogeneDB ID:

retro_cfam_431

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:11:60346092..60347261(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT6A
Ensembl ID:ENSCAFG00000010149
Aliases:None
Description:chaperonin containing TCP1, subunit 6A (zeta 1) [Source:HGNC Symbol;Acc:1620]


Retrocopy-Parental alignment summary:






>retro_cfam_431
TTGAACAGACTCGTTTCTGGTGCTGCAGACATCAAGCTTACTAAAGATGACAATGTGCTTCTTCATGAAATGCAAATTCA
GCACCCAACAGCCTCCCTAATAGCCAAAGTAGCAACAGCCCAGGACGACATAACTGGTGATGGTACCACTCCCAATGTCC
TAATCATTGGAGAGCTACTGAAACAGGCGGATCTCTACATTTCTGAAGGTCTTCATCCCAGAATAATAACAGAAGGATTT
GAAGCTGCAAAGGAAAAGGCACCTCAGTTTTTGGAACAAGTCAAAGTAAGCAAAGAAATGATAAAGAAATGGTAGATGTG
GCCAGAACATTTCTACTTACTAAAGTGCATGCTGAACTTGCTGATGTCTTAACAGAGGCTATAGTGGACTCGATTTTGAC
CATTAGAAAACAAGATGAACCTATCAATCTCTTCATGGTTGAGACCATGGAGATGAAACATAAATCTGAAACTGATACAA
GCTTAATCAGAGGTCTTGTTTTGGACCACGGGGCAAGGCATCCTGATATGAAAAAAAGGGTAGAAGATGCATACATCCTC
ACATGCAATGTGTAGTTAGAGTATGAAAAAACAGAAGTGAATTCTGGATTTTTTTTACAAGAGTGAAGAAGAGAGAGAGA
AACGTAAAAGCTGAAAGAAAATTCATTGAAGATAGAGTTAAAAAAAATAATAGAACTGGAAAAGAAAGTCTGTGGTGATT
CAGATAAAGGATTCATTGTTATTAATCAAAAGGGACTTGACCCCTTTTCCTTAGATGCTCCTGCAAAAGAAGGCTTAGTA
GCTCTGCATAGAGCTACAAGGAGAAATATGGAAAGGCTGACTCTTGATTGTGGTGGAGTAGCTCTAAATTCTATCGATGA
CCTAAATTCTGATTGTTTGGGACATGCAGGACTTGTCTATGAGTATACATTGGGAGAAGAGAAATTCACTTTTATTGAGA
AATGTAACAATCTTCGCTGCATCACATTATTGATCAAAGGACCAAATAAGCACACGCTCACTCAAATCAAAGATGCAATA
AGAGATGGCTTAAGGGCTGTTAAAAATGCTATTGATGATGGCTGTGTAGTTCCCGGTGTGGGTGCAGTTGAAGTGGCAAT
GGCAGAAGACTTGATTAAATATGAGCCCAGAGTAAAGGGGAGGGCCCAG

ORF - retro_cfam_431 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.55 %
Parental protein coverage: 73.77 %
Number of stop codons detected: 1
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMKMLVSGAGDIKLTKDGNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTSNVLIIGELLKQADLYISEG
...LVSGA.DIKLTKD.NVLLHEMQIQHPTASLIAKVATAQDDITGDGTT.NVLIIGELLKQADLYISEG
RetrocopyLNRLVSGAADIKLTKDDNVLLHEMQIQHPTASLIAKVATAQDDITGDGTTPNVLIIGELLKQADLYISEG
ParentalLHPRIITEGFEAAKEKALQFLEQVKVSKEM-DRETLIDVARTSLRTKVHAELADVLTEAVVDSILAIKKP
LHPRIITEGFEAAKEKA.QFLEQVKVSKEM.D.E...DVART.L.TKVHAELADVLTEA.VDSIL.I.K.
RetrocopyLHPRIITEGFEAAKEKAPQFLEQVKVSKEM<DKE-MVDVARTFLLTKVHAELADVLTEAIVDSILTIRKQ
ParentalDEPIDLFMVEIMEMKHKSETDTSLIRGLVLDHGARHPDMKKRVEDAYILTCNVSLEYEKTEVNSGFFYKS
DEPI.LFMVE.MEMKHKSETDTSLIRGLVLDHGARHPDMKKRVEDAYILTCNV.LEYEKTEVNSG.....
RetrocopyDEPINLFMVETMEMKHKSETDTSLIRGLVLDHGARHPDMKKRVEDAYILTCNV*LEYEKTEVNSGXXXQE
Parental-AEEREKLVKAERKFIEDRV-KKIIELKKKVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRN
....RE..VKAERKFIEDRV....IEL.KKVCGDSDKGF.VINQKG.DPFSLDA.AKEG.VAL.RA.RRN
Retrocopy<VKKRERNVKAERKFIEDRV>XXXIELEKKVCGDSDKGFIVINQKGLDPFSLDAPAKEGLVALHRATRRN
ParentalMERLTLACGGVALNSFDDLNPDCLGHAGLVYEYTLGEEKFTFIEKCNNPRSVTLLIKGPNKHTLTQIKDA
MERLTL.CGGVALNS.DDLN.DCLGHAGLVYEYTLGEEKFTFIEKCNN.R..TLLIKGPNKHTLTQIKDA
RetrocopyMERLTLDCGGVALNSIDDLNSDCLGHAGLVYEYTLGEEKFTFIEKCNNLRCITLLIKGPNKHTLTQIKDA
ParentalIRDGLRAVKNAIDDGCVVPGAGAVEVAMAEALIKYKPSVKGRAQ
IRDGLRAVKNAIDDGCVVPG.GAVEVAMAE.LIKY.P.VKGRAQ
RetrocopyIRDGLRAVKNAIDDGCVVPGVGAVEVAMAEDLIKYEPRVKGRAQ

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
SRP012049_cerebellum 0 .00 RPM 88 .74 RPM
SRP017611_brain 0 .00 RPM 68 .83 RPM
SRP017611_kidney 0 .00 RPM 81 .82 RPM
SRP017611_liver 0 .00 RPM 33 .21 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_431 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_431 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_431 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160771 retrocopy
retro_amel_855,
Canis familiaris ENSCAFG00000010149 1 retrocopy
retro_cfam_431 ,
Canis familiaris ENSCAFG000000182981 retrocopy
retro_cfam_342,
Choloepus hoffmanni ENSCHOG000000006543 retrocopies
retro_chof_1183, retro_chof_1193, retro_chof_150,
Callithrix jacchus ENSCJAG000000212792 retrocopies
retro_cjac_1320, retro_cjac_580,
Dipodomys ordii ENSDORG000000012491 retrocopy
retro_dord_617,
Felis catus ENSFCAG000000276542 retrocopies
retro_fcat_1102, retro_fcat_320,
Homo sapiens ENSG000001467312 retrocopies
retro_hsap_2741, retro_hsap_3290,
Gorilla gorilla ENSGGOG000000114391 retrocopy
retro_ggor_133,
Loxodonta africana ENSLAFG000000127911 retrocopy
retro_lafr_808,
Macaca mulatta ENSMMUG000000152721 retrocopy
retro_mmul_2582,
Monodelphis domestica ENSMODG000000065651 retrocopy
retro_mdom_1330,
Nomascus leucogenys ENSNLEG000000156641 retrocopy
retro_nleu_1355,
Oryctolagus cuniculus ENSOCUG000000176741 retrocopy
retro_ocun_468,
Procavia capensis ENSPCAG000000155321 retrocopy
retro_pcap_263,
Pongo abelii ENSPPYG000000258201 retrocopy
retro_pabe_2719,
Pan troglodytes ENSPTRG000000192062 retrocopies
retro_ptro_1854, retro_ptro_2225,
Pteropus vampyrus ENSPVAG000000014211 retrocopy
retro_pvam_663,
Rattus norvegicus ENSRNOG000000009231 retrocopy
retro_rnor_2226,


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