RetrogeneDB ID:

retro_vpac_125

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_1955:358432..359332(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NUDT9
Ensembl ID:ENSVPAG00000004012
Aliases:None
Description:nudix (nucleoside diphosphate linked moiety X)-type motif 9 [Source:HGNC Symbol;Acc:8056]


Retrocopy-Parental alignment summary:






>retro_vpac_125
ATGTCAGTGTCAGATGGCGCTGCCGACACCCCCCACAAGAAGGCCAGGACATCTCCGTACCCTGGCTCTACAGTAGAAAG
AACTGCAGTCCCCGACGAGAAAGTGAGCTGGCTGGTTGAGCGGCCAGAGTACAAGCCTGTCGAGTACACTTCTGGCTCTG
TCTTGGCCAGACCCTTTTGGGCAGATCCCCGAGTCGGGGAAAGGAACTTCTCTCCTAAATTTAACGAAAAGGATGGGCAT
GTTGAGAGAAGGAGCCGGACCGGTTTGTATGAGGTTGAAAACGGTAGACCCAGAAATCCTGCAGGTCGGATAGGGCTGGT
TGGCAGAGGGCTCCTGGAGCGTTGGGGTCCCAGTCAGGCTGCAGATCCCATCTTAACCAGGTGGAAAAACGATGGCAAGG
GAAATAGAGTTATCCACCCGGTTTCTGGGAGAAACATCCTGCAATTTGTGGCCATCAAAAGGAAAGACTGTGGAGAATGG
GCCATCCCTAGGGGGATAGTGGATCCCGGAGAGAAGATTAGTAGCTCCTCTTCAGTGAGGAAATTTGGTGAGGAAGCCAT
GAACTCCCTACAGAAATCCGAAACAGAAGCACAGGAGTTGGAGAAACAGCTGCACAAACTATTCAGCTAGGAACACTTTG
TGGTCTATAAAGGCTATGTGGATGACCCCCGAAACACGGATAACGCATGGATGGAGACAGAGGCTGTGAATTACCATGAG
GAGACAGGGGAGGTAATGGCTCATCTTCCTTTGGAAGCTGGTGATGATGCCAAGAAAGTAAGATGGGTGGACATTAATGA
TAAACTCAAACTTTATGCCAGCCACTCCTAATTTATTCAGCTTGTGGCTGAGAAACGAGGTGCCCACTGGAGGGAAGACG
TGTCTCCTGACTGCCATGGA

ORF - retro_vpac_125 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71. %
Parental protein coverage: 85.17 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSVSNCTKENSHNKARTSPYPGSKVQRSQVPNEKVGWLVEWQDYNPVEYTAVSVLAGPRWADPQISESNF
MSVS.......H.KARTSPYPGS.V.R..VP.EKV.WLVE...Y.PVEYT..SVLA.P.WADP...E.NF
RetrocopyMSVSDGAADTPHKKARTSPYPGSTVERTAVPDEKVSWLVERPEYKPVEYTSGSVLARPFWADPRVGERNF
ParentalSPKFNEKDGHIER-SQNGLYEI-NGRPRNPAGRTGLTGRGLLGRWGPNHAADPIITRWKRDRSGNKITNP
SPKFNEKDGH.ER.S..GLYE..NGRPRNPAGR.GL.GRGLL.RWGP..AADPI.TRWK.D..GN....P
RetrocopySPKFNEKDGHVERRSRTGLYEVENGRPRNPAGRIGLVGRGLLERWGPSQAADPILTRWKNDGKGNRVIHP
ParentalISGKNILQFVAIKRKDCGEWALPGGMVHPGEKITAT--LKRFGE-ALNSLQIS-AEKRELE-ELHKLFSQ
.SG.NILQFVAIKRKDCGEWA.P.G.V.PGEKI........FGE.A.NSLQ.S..E..ELE..LHKLFS.
RetrocopyVSGRNILQFVAIKRKDCGEWAIPRGIVDPGEKISSSSSVRKFGEEAMNSLQKSETEAQELEKQLHKLFS*
ParentalEHLVIYKGYVDDPRNTDNAWIETEAVNYHDETGEIMDNLTLEAGDDAGKVKWVDISDKLKLYASHSEFIK
EH.V.YKGYVDDPRNTDNAW.ETEAVNYH.ETGE.M..L.LEAGDDA.KV.WVDI.DKLKLYASHS.FI.
RetrocopyEHFVVYKGYVDDPRNTDNAWMETEAVNYHEETGEVMAHLPLEAGDDAKKVRWVDINDKLKLYASHS*FIQ
ParentalLVAEKRDAHWSEDSETDCHG
LVAEKR.AHW.ED...DCHG
RetrocopyLVAEKRGAHWREDVSPDCHG

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_125 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_125 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 22 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000032441 retrocopy
retro_amel_612,
Bos taurus ENSBTAG000000113541 retrocopy
retro_btau_1112,
Canis familiaris ENSCAFG000000095291 retrocopy
retro_cfam_1271,
Callithrix jacchus ENSCJAG000000061591 retrocopy
retro_cjac_1047,
Equus caballus ENSECAG000000195561 retrocopy
retro_ecab_123,
Echinops telfairi ENSETEG000000191641 retrocopy
retro_etel_348,
Felis catus ENSFCAG000000033151 retrocopy
retro_fcat_1509,
Homo sapiens ENSG000001705021 retrocopy
retro_hsap_709,
Gorilla gorilla ENSGGOG000000147771 retrocopy
retro_ggor_602,
Loxodonta africana ENSLAFG000000113911 retrocopy
retro_lafr_224,
Macropus eugenii ENSMEUG000000121234 retrocopies
retro_meug_1072, retro_meug_1345, retro_meug_1758, retro_meug_2162,
Monodelphis domestica ENSMODG000000207382 retrocopies
retro_mdom_157, retro_mdom_706,
Mustela putorius furoENSMPUG000000022581 retrocopy
retro_mputfur_585,
Nomascus leucogenys ENSNLEG000000095201 retrocopy
retro_nleu_464,
Oryctolagus cuniculus ENSOCUG000000026702 retrocopies
retro_ocun_1045, retro_ocun_990,
Ochotona princeps ENSOPRG000000040551 retrocopy
retro_opri_1152,
Pongo abelii ENSPPYG000000149141 retrocopy
retro_pabe_613,
Pan troglodytes ENSPTRG000000162591 retrocopy
retro_ptro_506,
Pteropus vampyrus ENSPVAG000000048291 retrocopy
retro_pvam_475,
Sus scrofa ENSSSCG000000092231 retrocopy
retro_sscr_447,
Tursiops truncatus ENSTTRG000000042071 retrocopy
retro_ttru_1549,
Vicugna pacos ENSVPAG00000004012 1 retrocopy
retro_vpac_125 ,




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