RetrogeneDB ID:

retro_vpac_72

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_1532:408829..410181(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TUBA1A
Ensembl ID:ENSVPAG00000005749
Aliases:None
Description:tubulin, alpha 1a [Source:HGNC Symbol;Acc:20766]


Retrocopy-Parental alignment summary:






>retro_vpac_72
ATGTGTGAGTGCATCTCCATCCATATTGGCCAAGCTGGTGTCCAGATCAGCAATGCCTGCTGGGAGCTCTACTGCCTGGA
ACACGGCATCCAGCCCAATGTCCAGATGCCAAGTGACAAGACCACTGGGGGAGGAGACGACTCCTTCAACACCTTCTTCA
GTGAGACAGGCACTGGCAAGCATGTGCCTAGGGCAGTGTTCGTAGACCTGGAACCCACAGTCATTGATGTTCGCACTGGC
ACCTACTGCCAGCTCTTCCACCCTAAGCAGCTCATCACAGGCAAAGAAGATGCTGCCAGCAACTATGCCCGCAGTCACTA
CATCATTGGCAAGGAGATCATTGACCTCATCTTGGACCGAATTCGGAAACTGGCTGACCAGTGCACAGGTCTTCAGGGGT
TCCTGGTTTTCCACAGCTTTTGTGGGGGAACTGGTTCTGGGTTTACCTCCCTGCTGGTGGAATGTCTCTCTGTCCATTAT
GGCAGGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCTCAGGTTTCCACAGCTATAGTTGAACCCTACAACTCCAT
CCTCACCACCCACACCACCCTGGAGCACTCTGACTGTGCTTTCATGGTAGACAATGAGGCCATCTATGACATATGTCGCA
GAAACCTCGATATTGAGCACCCAACCTGCACAAACCTGAATAGGCTGATAGGTCAAATTGTGTCCTCCGTCACCACTTCC
CTGAGGTTTGATGGAGCCCTGAATGTCAACTTGACAGAATTCCAAACCAATCTGGTACCCTATCCTCGCATCCACTTCCC
TCTGGCCACATATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGGTCACCAACGCTT
GCTTTGAGCCAGCCAACCAGATGGTGAAATGCGACCCTCGCCATGATAAATACATGGCTTGCTGCCTGTTGTACCATGGT
GACGTGGTCCCCAAAGATGTCAGTGCTGCCATTGCCACCATCAAGACAAGCGTACTATCCAGTTTGTGGACTGGTGCCCC
ACTGGCTTCAAAGTTAGTGTTAATTACCAGCCTCCCACCGTGGTACCTGGTGGAGACCTGGCCAAAGTACAGCGAGCTGT
GTGCATGCTGAGCAACACCACCGCCAGTGCTGAGGCCTGGGCTCGCCTGAACCACAAGTCTGACCTGATGTGTGCCAAGC
GTGCCTTGGTTCACGGGTACGTGGGTGAGGGCATGGAGGAAGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTGCCCTT
GAGAAGAATTATGAGGAGGTTGGTGTAGATTCTATTGAAGGAGAAGAAGAGGAAGGAGGAGAGGAACACTCA

ORF - retro_vpac_72 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.18 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
M.ECISIH.GQAGVQI.NACWELYCLEHGIQP..QMPSDKT.GGGDDSFNTFFSETG.GKHVPRAVFVDL
RetrocopyMCECISIHIGQAGVQISNACWELYCLEHGIQPNVQMPSDKTTGGGDDSFNTFFSETGTGKHVPRAVFVDL
ParentalEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
EPTVID.VRTGTY.QLFHP.QLITGKEDAA.NYAR.HY.IGKEIIDL.LDRIRKLADQCTGLQGFLVFHS
RetrocopyEPTVID-VRTGTYCQLFHPKQLITGKEDAASNYARSHYIIGKEIIDLILDRIRKLADQCTGLQGFLVFHS
ParentalFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVELYNSILTTHTTLEHSDCAFMVDNEAIY
F.GGTGSGFTSLL.E.LSV.YG.KSKLEFSIYPAPQVSTA.VE.YNSILTTHTTLEHSDCAFMVDNEAIY
RetrocopyFCGGTGSGFTSLLVECLSVHYGRKSKLEFSIYPAPQVSTAIVEPYNSILTTHTTLEHSDCAFMVDNEAIY
ParentalDICRRNLDIERPTYTNLNRLIGQIVSSITASLRFDGALNVNLAEFQTNLVPHPRIHFPLATYAPVISAEK
DICRRNLDIE.PT.TNLNRLIGQIVSS.T.SLRFDGALNVNL.EFQTNLVP.PRIHFPLATYAPVISAEK
RetrocopyDICRRNLDIEHPTCTNLNRLIGQIVSSVTTSLRFDGALNVNLTEFQTNLVPYPRIHFPLATYAPVISAEK
ParentalTYQEQLSVAEITNACFEPANEMVKCDPRHGKYIACCLLYHGDVVPKDVNAAIATIKT-KRTIQFVDWCPT
.Y.EQLSVAE.TNACFEPAN.MVKCDPRH.KY.ACCLLYHGDVVPKDV.AAIATIKT.KRTIQFVDWCPT
RetrocopyAYHEQLSVAEVTNACFEPANQMVKCDPRHDKYMACCLLYHGDVVPKDVSAAIATIKT<KRTIQFVDWCPT
ParentalGFKVGINYQPPTVVPGGDLAKVQRALCMLSNTTASAEAWACLDHKSDLMYAKRAFVHWYVGEGMEEGEFS
GFKV..NYQPPTVVPGGDLAKVQRA.CMLSNTTASAEAWA.L.HKSDLM.AKRA.VH.YVGEGMEEGEFS
RetrocopyGFKVSVNYQPPTVVPGGDLAKVQRAVCMLSNTTASAEAWARLNHKSDLMCAKRALVHGYVGEGMEEGEFS
ParentalEAREDMAALEKDYEEVGVDSVQGEGEEEGEEYS
EAREDMAALEK.YEEVGVDS..GE.EE.GEE.S
RetrocopyEAREDMAALEKNYEEVGVDSIEGEEEEGGEEHS

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






RNA-Seq - click to see more details

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Vicugna pacos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_vpac_72 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_72 was not experimentally validated.

Retrocopy orthology:
Vicugna pacos 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 10 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000014893 retrocopies
retro_btau_251, retro_btau_350, retro_btau_929,
Callithrix jacchus ENSCJAG000000208942 retrocopies
retro_cjac_1209, retro_cjac_3157,
Dasypus novemcinctus ENSDNOG000000041211 retrocopy
retro_dnov_43,
Equus caballus ENSECAG000000137981 retrocopy
retro_ecab_223,
Homo sapiens ENSG000001675521 retrocopy
retro_hsap_3313,
Nomascus leucogenys ENSNLEG000000178362 retrocopies
retro_nleu_245, retro_nleu_2757,
Oryctolagus cuniculus ENSOCUG000000278121 retrocopy
retro_ocun_197,
Pteropus vampyrus ENSPVAG000000046452 retrocopies
retro_pvam_1283, retro_pvam_414,
Rattus norvegicus ENSRNOG000000045593 retrocopies
retro_rnor_1200, retro_rnor_2006, retro_rnor_446,
Vicugna pacos ENSVPAG00000005749 4 retrocopies
retro_vpac_157, retro_vpac_210, retro_vpac_429, retro_vpac_72 ,


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