RetrogeneDB ID:

retro_ogar_2698

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873650.1:5341430..5343051(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT7
Ensembl ID:ENSOGAG00000009162
Aliases:None
Description:chaperonin containing TCP1, subunit 7 (eta) [Source:HGNC Symbol;Acc:1622]


Retrocopy-Parental alignment summary:






>retro_ogar_2698
ATGCCCACACCAGTTATTCTGTTGAAAGAGGGGACTGATAGCTCCCAAGGCATTCCCCTACTTGTGGGTAACATCAATGC
CCACCAGATGATTGCTGAGGCTGTAAGAATCACCCTGGGTCCCCACGGCATGGACAAGCTTATTGTGGATGGCTGAGGCA
AATCAACAATTTCTAACGATGGGGCCACAATTCTGAAACTCCTTGATGTTGTCTATCCTGCAGCAAAGACTCTACTGAAC
ATTGCCAAATCTCAAGATGCAGAGGTTGGTGATGGCACCACCTCAGTGACCTTGCTGGCTGCAAAGTTTCTGAAGCAGGT
GAAACCATACGTGGAGGAAGGTTTTCACCCCCAGATCATCATTCAAGCTTTCCGAATAGCCACTCAGTTAGCAGTTAAGA
AGATCAAAGAGATTGCGTGACAATGGATGAAGAAGACAGATAAAGTAGAGAGGAGGAAGCTGCTGGAGAAGTGTGCCATG
ATTGGTCTGAGTTCCAAGCTGATTTCCCAGCAGAATGACTTTGCTAAGATGGTGGTTGATGCAGTGATGATGCTTGATGA
TTTGTTGCAGCTTAAAATGATGGGAATCAAGAAGGTACAGGGTGGAGCCCTAGAGGACTCTCAGCTGGTAGCTGGTGTTG
CATTCAAGAAGACTTTCTTTTATGCTGGGTTTGAAATGCAACCCCAAAAGTACAATATTCCCATGATTGCCCTTTTAAAT
GTTGAGCTCGGGTTGAAAGCTGAGAAAGATAACGCCGAGATCAGAGTCCACCTAGCTGCGGATTATCAGATTACTGTTGA
TGCTGAGTGGAACAATCTTTACGACAAGTTAGAGAGGATCCATCATTCTGGGGCCAAAATTATCTTGTCCAAATCCCCAT
TGGAGATGTGGCCACCCCCTACATGGCTGACAGGGACAAGTTTTGTGCTGGCCAAGTACCTGAGGAGGATCTGAAGAGGA
CAATGATGGCCTGTGGAGGCTCACTCCAGACCAGTATGAGTGCTCTGCCAGCAAATGTGCTGGGTCACTGTCAGGTGTTT
GAAGAAACTCAGATTGAAGGTTAAAGGTACAATTTTTTCACTGTCTGCCCCAAGGCCAAGGCACGCACCTTCATCCTCTG
TGGCAGTGCCCAGCAGTTTATGGAGGAAATGGAGTGGTCCCTGCATGAAGCCATCATCATGGTCAGGTGGACCATCAAGA
ATGTTTCAGTGGTGGCTGGTGGCAGGGCCATTGAGATGGAGCTCTTCATGTACCTGTGGGTTTGCCTAAGGACTATTCCA
GGAAAGCAGCAGCAGCTGTTGACTGGGATGTATGCCAAGGCCTTGAAGATTATCCCACTCCAGCTGTGTAATAATGCTGG
TTTGATGCTACAAACATCCTCAATAAGATGTGGGCTTAGTATGACCAGGGGGCAGATGGTATGGGGTGGACATCAAGAAT
GAGGACATTGCTGGCAAATTTGAGGCCTTCGTGTGGGAGCCAGCTATGGTGCAGATCAATGTCCTGACAGCAGCCTTGGA
GGCGGTAAGCGTTATTGTGCCCTAGATGAAATCAAGAACCCAGGCTTGACTGTGGCCACTCTCCTAGCAGCTGGCCAGGG
TGAGGTCGTGGCTGCCCCATT

ORF - retro_ogar_2698 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.23 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMPTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDV
MPTPVILLKEGTDSSQGIP.LV.NI.A.Q.IAEAVR.TLGP.GMDKLIVDG.GK.TISNDGATILKLLDV
RetrocopyMPTPVILLKEGTDSSQGIPLLVGNINAHQMIAEAVRITLGPHGMDKLIVDG*GKSTISNDGATILKLLDV
ParentalVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVKKIKEIA-
V.PAAKTL..IAKSQDAEVGDGTTSVTLLAA.FLKQVKPYVEEG.HPQIII.AFR.ATQLAVKKIKEIA.
RetrocopyVYPAAKTLLNIAKSQDAEVGDGTTSVTLLAAKFLKQVKPYVEEGFHPQIIIQAFRIATQLAVKKIKEIA*
ParentalVTVKKTDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGALEDSQL
...KKTDKVE.RKLLEKCAM..LSSKLISQQ..F.AKMVVDAVMMLDDLLQLKM.GIKKVQGGALEDSQL
RetrocopyQWMKKTDKVERRKLLEKCAMIGLSSKLISQQNDF-AKMVVDAVMMLDDLLQLKMMGIKKVQGGALEDSQL
ParentalVAGVAFKKTFSYAGFEMQPKKYDNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLER
VAGVAFKKTF.YAGFEMQP.KY..PMIALLNVEL.LKAEKDNAEIRVH...DYQ..VDAEWN.LYDKLER
RetrocopyVAGVAFKKTFFYAGFEMQPQKYNIPMIALLNVELGLKAEKDNAEIRVHLAADYQITVDAEWNNLYDKLER
ParentalIHRSGAKVVLSK-LPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRCQVFE
IH.SGAK..LSK..PIGDVAT.Y.ADRD.FCAG.VPEEDLKRTMMACGGS.QTS..AL.A.VLG.CQVFE
RetrocopyIHHSGAKIILSK<IPIGDVATPYMADRDKFCAGQVPEEDLKRTMMACGGSLQTSMSALPANVLGHCQVFE
ParentalETQIGGERYNFFTGCPKAKTCTFILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKY
ETQI.G.RYNFFT.CPKAK..TFIL.G.A.QFMEE.E.SLH.AI..VR..IKN.SVVAGG.AIEMEL..Y
RetrocopyETQIEG*RYNFFTVCPKAKARTFILCGSAQQFMEEMEWSLHEAIIMVRWTIKNVSVVAGGRAIEMELFMY
ParentalLRDYSRTIPGK-QQLLIGAYAKALEIIPRQLCDNAG-FDATNILNKLRARHAQ-GGTWYGVDINNEDITD
L....RTIPGK.QQLL.G.YAKAL.IIP.QLC.NAG.FDATNILNK..A...Q.GG.WYGVDI.NEDI..
RetrocopyLWVCLRTIPGKQQQLLTGMYAKALKIIPLQLCNNAG<FDATNILNKMWA*YDQ<GGRWYGVDIKNEDIAG
ParentalNFEAFVWEPAMVRINALTAASEAACLIV-SVDETIKNPRSTVDTPPAAGRGR-GRGRPL
.FEAFVWEPAMV.IN.LTAA.EA...IV...DE.IKNP..TV.T..AAG.G..GRG.P.
RetrocopyKFEAFVWEPAMVQINVLTAALEAVSVIV<ALDE-IKNPGLTVATLLAAGQGE<GRGCPI

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_2698 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 15 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000088791 retrocopy
retro_cfam_151,
Choloepus hoffmanni ENSCHOG000000079371 retrocopy
retro_chof_2313,
Cavia porcellus ENSCPOG000000198691 retrocopy
retro_cpor_1458,
Echinops telfairi ENSETEG000000094092 retrocopies
retro_etel_1478, retro_etel_607,
Homo sapiens ENSG000001356241 retrocopy
retro_hsap_3354,
Gorilla gorilla ENSGGOG000000077661 retrocopy
retro_ggor_2274,
Macropus eugenii ENSMEUG000000004161 retrocopy
retro_meug_1995,
Macaca mulatta ENSMMUG000000124481 retrocopy
retro_mmul_2093,
Nomascus leucogenys ENSNLEG000000104141 retrocopy
retro_nleu_1175,
Otolemur garnettii ENSOGAG00000009162 2 retrocopies
retro_ogar_2001, retro_ogar_2698 ,
Pongo abelii ENSPPYG000000122971 retrocopy
retro_pabe_2760,
Pan troglodytes ENSPTRG000000120601 retrocopy
retro_ptro_2133,
Rattus norvegicus ENSRNOG000000156302 retrocopies
retro_rnor_2179, retro_rnor_535,
Sorex araneus ENSSARG000000114751 retrocopy
retro_sara_539,
Tupaia belangeri ENSTBEG000000020662 retrocopies
retro_tbel_3708, retro_tbel_3751,


Copyright © RetrogeneDB 2014-2017