RetrogeneDB ID:

retro_vpac_231

Retrocopy
location
Organism:Alpaca (Vicugna pacos)
Coordinates:GeneScaffold_3060:569502..570496(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSVPAG00000003069
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSVPAG00000001963
Aliases:None
Description:choroideremia (Rab escort protein 1) [Source:HGNC Symbol;Acc:1940]


Retrocopy-Parental alignment summary:






>retro_vpac_231
TTTGTGCAGTCCTCATTTTCAGAATACTTAAAAACCAAAAAATTAACCCCCAACCTCCAGCATTTTGTACTACATTCAAT
TGCAATGATGTCGGAGTCACCTTGCACTACAATAGATGGCCTTAAAGCAACAAAGAACTTTCTTCAGTGTCTTGGACGGT
TTGGCAACACTCCCTTTTTACTTCCCTTGTATGGCCAAGGCGAAATTCCCCAGTGTTTCTGCAGAATGTGTGCAGTCTTT
GGTGGAGTCTATTGTCTTCGCCATAAAGTACAATGCCTTGTAGTTGACAAAGAATCTGGAAGATGTAAAGCAATTATAGA
TCACTTTGGTCGAAGAATAAGTGCTAAATATTTCATTGTGGAGGATAGTTACCTTTCTGAGGAAACATGCTTAAATGTGC
AGTACAAGCAGATCTCCAGGGCAGTGCTCATTACGGACCAGTCTGTACTAAAGGCAGAGTCAGATCAGCAGATTTCCGTT
TTGATAGTGCCTCCAGTGGAACCAGGAGCATGTGCTATTCGCATCACTGAACTGTGTTCTTCAACCATGACATGCATGAA
AGACACCTATCTGGTACATCTGACCTGTTCATCTTCTAAAACAGCAAGAGAAGACTTAGAATCAGTGGTGAAGAAATTAT
TTACCCCATATGCTGAAACAGAGATAGACAAGGAAGAACTTAAAAAGCCAGGACTCTTGTGGGCTCTTTATTTTAATATG
AGAGATTCCTCAGGAGTCAGCAGAAGCTCATATAATGGCTTGCCTTCCAATGTTTATGTCTGCACTGGGCCTGACTGTGG
ACTAGGAAGTGAGCATGCAGTCAAGCAAGCTGAAACACTGTTCCGGGGAGATCTTTCCAAGTGAGGAATTCTGCCCACCA
CCTCCAAATCCAGAAGACATTTTCTTTGAGGGTGATGACAAGCAGCCAGAGCCTTCTGGAACCAGTAACATAGTGATGGC
CAAACTAGAATCCTCTGAGGGAAGCAAAAACCTA

ORF - retro_vpac_231 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.1 %
Parental protein coverage: 50.69 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYEEISFSEYLKTQKLTPNLQYFVLHSIAMTSETASSTIDGLKATRNFLHCLGRYGNTPFLFPLYGQGELP
....SFSEYLKT.KLTPNLQ.FVLHSIAM.SE....TIDGLKAT.NFL.CLGR.GNTPFL.PLYGQGE.P
RetrocopyFVQSSFSEYLKTKKLTPNLQHFVLHSIAMMSESPCTTIDGLKATKNFLQCLGRFGNTPFLLPLYGQGEIP
ParentalQCFCRMCAVFGGIYCLRHSVQCLVVDKESGRCKAIIDHFGQRIISKHFLVEDSYFSENTCSRVQYRQISR
QCFCRMCAVFGG.YCLRH.VQCLVVDKESGRCKAIIDHFG.RI..K.F.VEDSY.SE.TC..VQY.QISR
RetrocopyQCFCRMCAVFGGVYCLRHKVQCLVVDKESGRCKAIIDHFGRRISAKYFIVEDSYLSEETCLNVQYKQISR
ParentalAVLITDRSVLKTDSDQQISILTVPAEEPGASAVRVIELCSSTMTCMKGTYLVHLTCTSSKTAREDLEPVV
AVLITD.SVLK..SDQQIS.L.VP..EPGA.A.R..ELCSSTMTCMK.TYLVHLTC.SSKTAREDLE.VV
RetrocopyAVLITDQSVLKAESDQQISVLIVPPVEPGACAIRITELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVV
ParentalQKLFTPYTETEIENEEVEKPRLLWALYFNMRDSSDISRNSYNDLPPNVYVCSGPDCGLGNDNAVKQAEAL
.KLFTPY.ETEI..EE..KP.LLWALYFNMRDSS..SR.SYN.LP.NVYVC.GPDCGLG...AVKQAE.L
RetrocopyKKLFTPYAETEIDKEELKKPGLLWALYFNMRDSSGVSRSSYNGLPSNVYVCTGPDCGLGSEHAVKQAETL
ParentalFQ-QICPNEDFCPPPPNPEDIILDGDSSQPESLESIAAPEANSETLKESANL
F...I.P.E.FCPPPPNPEDI...GD..QPE.........A..E....S.NL
RetrocopyFR>EIFPSEEFCPPPPNPEDIFFEGDDKQPEPSGTSNIVMAKLESSEGSKNL

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_231 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_231 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 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG000000167761 retrocopy
retro_mmul_460,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG00000001963 1 retrocopy
retro_vpac_231 ,




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