RetrogeneDB ID:

retro_pvam_663

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_608:635936..637153(+)
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:ENSPVAG00000001421
Aliases:None
Description:chaperonin containing TCP1, subunit 6A (zeta 1) [Source:HGNC Symbol;Acc:1620]


Retrocopy-Parental alignment summary:






>retro_pvam_663
AGAAAAAAGGCACTTCAGTTTCTGCATGTTAAAGTAAGCAAAGAGATGAGCAGGGAAACAGTCATTGATGTGGCCAGAAC
ATCTCTACCTGCTAAAGTTCCTGCTGAACTTGCTAATGTCTTATTAACAGAGGCTGTAGCTGACTCCATCTTGGCCATTA
AAAAATGAGATGAACCTATGGACCTCTTTGTGGTTGAGATCATGAAGATGAAACATAAATCTGAAACACACACAAGCTTA
ATCAGAGGTCTCATTTTGGACCATGGGCACGGCATCCGGATATGAAAAAAATAGTAGAAGAAGATGCATACATTTTCATG
TACAATGTGTCACTGGAATGTGAAAAAACAGAAGTACATTCTGGCTTTTTTTTTTTTTTACTAGAGTACAGAAGAGAGAG
AGAGACTAGTAAAAGCTGAAAGAAAACTCATGAAGATAAAGTTTAAAAAATAGAGCTGAAAAAGAAAGTCTGTCATGACT
CAGATAAAGAATTTGTTGTTTTTAATCAAAAAGTAATTGACCCATTTTCCTTAGATGCTCTTGCAAAAAAATGCATAGTA
GCTCTATGCAGAGCTAAAAGGAGAAATATGGAAAGGCTGACTCTAGCTTGTGGTGGAGTAGCTCTAAATTCTTTTGATGA
CCTAAATCCTGATGGTTTGGGACATGCAGGACTTGTCTATGAGTATACATTAGGAGAAAAGAAGTTCACCTTTATGGACA
AATGTAACAATCCTTGCTCTGTCATGTTATTGGTCAAAGGACCAAATAAGCACACATTCGCTCAAATCAAAGATGCAATA
AGAGATGGCCTGAGGGCTGTTACAAATGCTGTTGATGATGGCTGTGTAGTTCCAGGAACCGGTGCAGTGGAAGTAGCAAT
GGCAGAAGCCCTGATAAACAGAAGCCCAGTTGAAAAGGGCAGGGCTCAACTTGGAATTCAAGCATTTGCTGATGCATTGC
TCATTATTCACAAAGTTCTTGCTCAGAATACTGGTTTTGACCTTCAGGAAACACTAGTTATAGTTCAAGCAGAACATTCA
AATTCAGATCAATTTGTGGGTGTGAATTCGATCGCAGGTGAGGCAATGGTAGCAGCAGAGATAGGCAGACGGAATAACCG
CTGTGTGAAGAAACAGCTTCACTCCTGCACTGTGATTGCCACCAACATCCTCCTGGTTGGTGAGACCGTGCAAGCAGGAA
CGTCTTCTCTGAAAGGT

ORF - retro_pvam_663 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.34 %
Parental protein coverage: 76.27 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalKEKALQFLEQIKVSKEMDRETLIDVARTSLRTKVHAELADVL-TEAVVDSILAIKKQDEPIDLFMVEIME
..KALQFL...KVSKEM.RET.IDVARTSL..KV.AELA.VL.TEAV.DSILAIKK.DEP.DLF.VEIM.
RetrocopyRKKALQFLH-VKVSKEMSRETVIDVARTSLPAKVPAELANVLLTEAVADSILAIKK*DEPMDLFVVEIMK
ParentalMKHKSETDTSLIRGLVLDHG-ARHPDMKKRV-EDAYILTCNVSLEYEKTEVNSGFFYKSAEER--EKLVK
MKHKSET.TSLIRGL.LDHG.ARHPDMKK.V.EDAYI...NVSLE.EKTEV.SG......E.R......K
RetrocopyMKHKSETHTSLIRGLILDHG<ARHPDMKKIVEEDAYIFMYNVSLECEKTEVHSGXXXXXLEYRRERETSK
ParentalAERKFIEDRVKKIIELKKKVCGDSDKGFVVINQKGIDPFSLDALAKEGIVALRRAKRRNMERLTLACGGI
...K..ED.V.K.IELKKKVC.DSDK.FVV.NQK.IDPFSLDALAK..IVAL.RAKRRNMERLTLACGG.
RetrocopyS*KKTHEDKV*K-IELKKKVCHDSDKEFVVFNQKVIDPFSLDALAKKCIVALCRAKRRNMERLTLACGGV
ParentalALNSFDELNPDCLGHAGLVYEYTLGEEKFTFIEKCNNPRSVTLLVKGPNKHTLTQIKDAIRDGLRAVKNA
ALNSFD.LNPD.LGHAGLVYEYTLGE.KFTF..KCNNP.SV.LLVKGPNKHT..QIKDAIRDGLRAV.NA
RetrocopyALNSFDDLNPDGLGHAGLVYEYTLGEKKFTFMDKCNNPCSVMLLVKGPNKHTFAQIKDAIRDGLRAVTNA
ParentalIDDGCIVPGAGAVEVAMAEALVKYKPTVKGRAQLGVQAFADALLIIPKVLAQNSGFDLQETLVKVQAEHS
.DDGC.VPG.GAVEVAMAEAL....P..KGRAQLG.QAFADALLII.KVLAQN.GFDLQETLV.VQAEHS
RetrocopyVDDGCVVPGTGAVEVAMAEALINRSPVEKGRAQLGIQAFADALLIIHKVLAQNTGFDLQETLVIVQAEHS
ParentalNSGQLVGVDLNTGEPMVAAEVGIWDNYCVKKQLLHSCTVIATNILLVDEIMRAGMSSLKG
NS.Q.VGV....GE.MVAAE.G...N.CVKKQ.LHSCTVIATNILLV.E...AG.SSLKG
RetrocopyNSDQFVGVNSIAGEAMVAAEIGRRNNRCVKKQ-LHSCTVIATNILLVGETVQAGTSSLKG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_663 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus 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 18 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000160771 retrocopy
retro_amel_855,
Canis familiaris ENSCAFG000000101491 retrocopy
retro_cfam_431,
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 ENSPVAG00000001421 1 retrocopy
retro_pvam_663 ,
Rattus norvegicus ENSRNOG000000009231 retrocopy
retro_rnor_2226,


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