RetrogeneDB ID:

retro_vpac_640

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:scaffold_900:435268..436020(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UQCRC2
Ensembl ID:ENSVPAG00000010914
Aliases:None
Description:ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]


Retrocopy-Parental alignment summary:






>retro_vpac_640
CCAGATGAGTTACATTACTATGCTCAGAACCGTTTTACAAGTGCAAGAATGGCTTTGATTGGCCTCCGTGTGAGTCATCC
CCGTTCTAAAAGCAAAGTTGCTAAATGGATCTCAATATGAGGCGTGGGCTTGGTCTATCTGGTGCAAAGGCCAAATACCG
TGGAGGTGAAATTCGAGAACAAAATGGAAACAGTCTCTTCCATGCTGCTCTTGCAGCAGAAAGTGCTGTGACAGGAGTGC
AGCAGCAAATGCATTTAGTGTTCTGCAGCACGTCCTCGGTGCTGAACCACGTTAAGAGGGGCAGCAATGACACCAGCTCT
CTGTACGAGGCTGTTGCCTAGGGAATTCACCAGCCATTTGATGTGTCTGATTTTAATGCCAGTTACTTAGATTCTAGACT
CTTTGGGATTTACACTATCTCACAAGCTGCAGCTGCTGGAGATGTTATCAAGGCTGCCTATAACTAAGTAAAAACAACTG
CTCAAGGAAACCATTCTAACACAGATGTCCAAGCTGCAAAGGACAAGCTGATTGCCGAGTATCTAATGTCAGTGGAGTCT
TCTGGGGGCTTCCTGGATGAAGTCAGGTGCCAGGCTCTAGTTGCTGGTTCATACATGCCACCAGGCAGAGTCCTTCAGCA
GGCTGACTCAGTAGCTGACCCTGATGTCATAAATGCTGCAAAGAAGTTTGTTTCTGGTCAGAAGTCAAAGGCAGCAAGTG
GACATTTGGGGCAGACAACTTTCGTTGATCAG

ORF - retro_vpac_640 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.94 %
Parental protein coverage: 56.79 %
Number of stop codons detected: 3
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalPDELHHYVQNHFTSARMALIGLGVSH-PVLK-QVAERFLNVRGGLGLSSAKAKYRGGEVREQNGDSLVHA
PDELH.Y.QN.FTSARMALIGL.VSH.PVLK.Q.....LN.R.GLGLS.AKAKYRGGE.REQNG.SL.HA
RetrocopyPDELHYYAQNRFTSARMALIGLRVSH>PVLK>QSC*MDLNMRRGLGLSGAKAKYRGGEIREQNGNSLFHA
ParentalALVAESTAAGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVAKGTHQPFDVSAFNASYSDSGLFGIY
AL.A...A..........V.........HVKRGSN.TSSLY.AVA.G.HQPFDVS.FNASY.DS.LFGIY
RetrocopyAL-AAESAVTGVQQQMHLVFCSTSSVLNHVKRGSNDTSSLYEAVA*GIHQPFDVSDFNASYLDSRLFGIY
ParentalTISQAAAAGDVIKAAYNQVKTIAQGNLSNTDVQTAKNKLKASYLMSVESSESFLDEIGSQALVAGSYVPP
TISQAAAAGDVIKAAYN.VKT.AQGN.SNTDVQ.AK.KL.A.YLMSVESS..FLDE...QALVAGSY.PP
RetrocopyTISQAAAAGDVIKAAYN*VKTTAQGNHSNTDVQAAKDKLIAEYLMSVESSGGFLDEVRCQALVAGSYMPP
ParentalSTVLQQIDAVADADVINAAKKFVSGRKSMAASGNLGHTPFVDE
..VLQQ.D.VAD.DVINAAKKFVSG.KS.AASG.LG.T.FVD.
RetrocopyGRVLQQADSVADPDVINAAKKFVSGQKSKAASGHLGQTTFVDQ

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_640 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_640 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 17 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000091161 retrocopy
retro_cjac_222,
Echinops telfairi ENSETEG000000010841 retrocopy
retro_etel_2087,
Homo sapiens ENSG000001407401 retrocopy
retro_hsap_2785,
Gorilla gorilla ENSGGOG000000153791 retrocopy
retro_ggor_1941,
Myotis lucifugus ENSMLUG000000033452 retrocopies
retro_mluc_1391, retro_mluc_770,
Macaca mulatta ENSMMUG000000182872 retrocopies
retro_mmul_1442, retro_mmul_683,
Monodelphis domestica ENSMODG000000076451 retrocopy
retro_mdom_327,
Mustela putorius furoENSMPUG000000168491 retrocopy
retro_mputfur_1042,
Nomascus leucogenys ENSNLEG000000121851 retrocopy
retro_nleu_685,
Oryctolagus cuniculus ENSOCUG000000038912 retrocopies
retro_ocun_604, retro_ocun_739,
Otolemur garnettii ENSOGAG000000054784 retrocopies
retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps ENSOPRG000000004191 retrocopy
retro_opri_455,
Pongo abelii ENSPPYG000000071741 retrocopy
retro_pabe_2232,
Pan troglodytes ENSPTRG000000078711 retrocopy
retro_ptro_1886,
Sorex araneus ENSSARG000000106701 retrocopy
retro_sara_231,
Tupaia belangeri ENSTBEG000000107851 retrocopy
retro_tbel_3988,
Vicugna pacos ENSVPAG00000010914 1 retrocopy
retro_vpac_640 ,


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