RetrogeneDB ID:

retro_ogar_2001

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873579.1:7320431..7322058(-)
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_2001
ATGCCCACAGCAGTTGTTCTGTTGAAAGAGGGGACTGATAGCTCCCAAGGCATTCCCCAGCTTGTGAGTAACATCAGTGC
CTGCCAGGTGATTGCCGAGGCTGTAAGAACCACCCTAGGTCCCTGTGGCATGGACAAGCTTTTTGTGGATGGCCAAGGCA
AAGCAATAATTTCTAATGATCAGGCCACAATTCTGAAACTCCTTAATGTTGTCCATCTTGCAGCAAAGACTTTAGTGGAC
ATTGCCAAATCTCAAGATGCTGAGGTTGGTGAGGGCACCATCTCAGTGACCTTGCTGGCTGCAGAGTTTCTGAAGCAGGT
GAAACCATATATGGAGGAAGGTTTGCATCCCCAGATCATCATTTGAGCTTTTCGCACAGCCACTCAGTTGGCAGTAGAGA
AGATCAAAGAGACTTCTGTGATGGTGAAGAAGACAGAAAAAGTGGAGCAGAGGAAGCTGCTGGAGAAGTGTGCCTTGACT
CCTCTGAGTTCCAAGCTGATCTCTCAGCAGAAAGCCTTCTTTGCTAAGATGGTGGTTGATGCAGTGATGATGCTTGATGA
TTTGTTGTAGCTTAAAATGATTGGAATCAAGAAGGTACAGGGTGGAGCCCTAAAGGATTCTCAGCTGGTAGCTGGTGTTG
CATTCAAGAAGACTTTCTCTTATGCTGGGTTTGAAAGGCAACCCAAAAAGTACGATAATCCCATGATTGCCCTTTTAAAT
GTTGAGCTCGAGTTGAAAGCTGAGAAAGATAATGCCAAGATCAGAGTCCATACGGTTGAGGATTATCAGGCTATTGTTGA
TGCTGAGTGGAACATTCTTTATGACAAGTTAGAGAGGATCTATCATTCTGGGGCCAAAGTTGTCTTGTCCCAACTCTCCA
TTGGAGATGTGGCCACCCAATACTTTGCTGACAAGGACATGTTCTGTGCTGGCCGAGTACCTGAGGAGGATCTGAAAAGG
ACAATGATGGCTTGCGGAGGCTCAATCCAGACCAGTGTGAGTGCTCTGTCAGCAGATGTGCTGGGTCACTGCCAGGTTTT
TGAAGAAACTCAGATTGGAGGTGAAAGGTACAATTTTTTCACTGGCTGCCCCAAGGCCAAGACATGCACCTTAATCCTCT
GCAGTGGTGCTGAGCAGTTTATGGAGGAAACAGAGCGGTCCCTGCATGATGCCATTATGATCGTCAGGAGGGCCATCAAG
AATGATTCGGTGGTAACCTGTGGTGGGGCCATTGAGATGGAGCTCTCCAAGTACCTGCAGGATCACTCAAGGACTATTTC
AGGAAAGCAGCAGCATTTGATTGGGGCATATGCCAAGGCCTTGGAGATTATCCCACACCAGCTGTGTGATAATGCTGGTT
TTGATGCTACAAACATCCTCAACAAGCTGCGGGCTCGGCATGCTCAGGGGGGCACATGGTATGGGGTGGACATCAACAAT
GAGGACATTACTGACAACTTTGAGGCCTTTGTGTGGGAGCCAGCTATGGTGCGGATCAATGCCCTGACAGCAGCCTCAGG
GGGCAGCATGCCTTATTGTCTCTGTAGATGAAACCATCAAGAACCCCCGTTCAACTGTGGACACTCCCCCAGCAGCTGGC
CGGGGCCGAGGTTGTGGCTACTCCCTT

ORF - retro_ogar_2001 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.53 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMPTPVILLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPRGMDKLIVDGRGKATISNDGATILKLLDV
MPT.V.LLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGP.GMDKL.VDG.GKA.ISND.ATILKLL.V
RetrocopyMPTAVVLLKEGTDSSQGIPQLVSNISACQVIAEAVRTTLGPCGMDKLFVDGQGKAIISNDQATILKLLNV
ParentalVHPAAKTLVDIAKSQDAEVGDGTTSVTLLAAEFLKQVKPYVEEGLHPQIIIRAFRTATQLAVKKIKEIAV
VH.AAKTLVDIAKSQDAEVG.GT.SVTLLAAEFLKQVKPY.EEGLHPQIII.AFRTATQLAV.KIKE..V
RetrocopyVHLAAKTLVDIAKSQDAEVGEGTISVTLLAAEFLKQVKPYMEEGLHPQIII*AFRTATQLAVEKIKETSV
ParentalTVKKTDKVEQRKLLEKCAMTALSSKLISQQKAFFAKMVVDAVMMLDDLLQLKMIGIKKVQGGALEDSQLV
.VKKT.KVEQRKLLEKCA.T.LSSKLISQQKAFFAKMVVDAVMMLDDLL.LKMIGIKKVQGGAL.DSQLV
RetrocopyMVKKTEKVEQRKLLEKCALTPLSSKLISQQKAFFAKMVVDAVMMLDDLL*LKMIGIKKVQGGALKDSQLV
ParentalAGVAFKKTFSYAGFEMQPKKYDNPMIALLNVELELKAEKDNAEIRVHTVEDYQAIVDAEWNILYDKLERI
AGVAFKKTFSYAGFE.QPKKYDNPMIALLNVELELKAEKDNA.IRVHTVEDYQAIVDAEWNILYDKLERI
RetrocopyAGVAFKKTFSYAGFERQPKKYDNPMIALLNVELELKAEKDNAKIRVHTVEDYQAIVDAEWNILYDKLERI
ParentalHRSGAKVVLSKLPIGDVATQYFADRDMFCAGRVPEEDLKRTMMACGGSIQTSVNALSADVLGRCQVFEET
..SGAKVVLS.L.IGDVATQYFAD.DMFCAGRVPEEDLKRTMMACGGSIQTSV.ALSADVLG.CQVFEET
RetrocopyYHSGAKVVLSQLSIGDVATQYFADKDMFCAGRVPEEDLKRTMMACGGSIQTSVSALSADVLGHCQVFEET
ParentalQIGGERYNFFTGCPKAKTCTFILRGGAEQFMEETERSLHDAIMIVRRAIKNDSVVAGGGAIEMELSKYLR
QIGGERYNFFTGCPKAKTCT.IL..GAEQFMEETERSLHDAIMIVRRAIKNDSVV..GGAIEMELSKYL.
RetrocopyQIGGERYNFFTGCPKAKTCTLILCSGAEQFMEETERSLHDAIMIVRRAIKNDSVVTCGGAIEMELSKYLQ
ParentalDYSRTIPGKQQLLIGAYAKALEIIPRQLCDNAGFDATNILNKLRARHAQGGTWYGVDINNEDITDNFEAF
D.SRTI.GKQQ.LIGAYAKALEIIP.QLCDNAGFDATNILNKLRARHAQGGTWYGVDINNEDITDNFEAF
RetrocopyDHSRTISGKQQHLIGAYAKALEIIPHQLCDNAGFDATNILNKLRARHAQGGTWYGVDINNEDITDNFEAF
ParentalVWEPAMVRINALTAAS-EAACLIVSVDETIKNPRSTVDTPPAAGRGRGRGRPL
VWEPAMVRINALTAAS..AACLIVSVDETIKNPRSTVDTPPAAGRGRG.G..L
RetrocopyVWEPAMVRINALTAAS>GAACLIVSVDETIKNPRSTVDTPPAAGRGRGCGYSL

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_2001 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