RetrogeneDB ID:

retro_pvam_1462

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_9241:34262..35284(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IGBP1
Ensembl ID:ENSPVAG00000005483
Aliases:None
Description:immunoglobulin (CD79A) binding protein 1 [Source:HGNC Symbol;Acc:5461]


Retrocopy-Parental alignment summary:






>retro_pvam_1462
ATGGCAGCAGCCAAAGAAGACGAGTTACTTCTACCTCGGCTTCCTGAGCTCTTTGAAACCAGCAAGCAGCTTCTAGACGA
AGTAGAAGTAGCAGCCGAACCCATCAGTTCCCGGATAATCCAAGAGAAGGTATTGAAGGGACTAGACCTCCTTAAGAAGG
CTGCCAAAATGTTATCTCAACTTGACTTGTTCAGCCAAAATGAAGATTTGGAAGAGATTGCTTCTACTGACCTGAAGTAC
CTGATGGTACCAGCATTTCAAGGAGCACTTGCCATGAAACAGGTCAACCCAAGTAAGCATCTAGATCATTTGCAGTGGGC
TCGAGAACACTTTTTAAACTACTTAACTCAGTGCCAATACTATCATGTGGCAGAATTTGAGTTGCCCAAAACCAAGAACA
ACTCAGCTGAAAATAACACTGCTAGTTCCTCCGTGACCTATTCTAGCCTCATTGCTATAACCTCTCAAAGACAGGCAAAA
ATAGAGAGATACAAGCAAAAGAAGGAAGTGGAACATAGGTTATCTGCACTGAAATCTGCTGTGGAAAGTGGTCAAGCTGA
TGATGAGAGTATTCGTGAATATTACCTCCTTCACCTTCAAAGATGGGATTGGTATCAGCTTAGAAGAGATTGAGAGCATT
GACCTGGAGATAAAGGTCCTGAGAGAAAAAGCCTCTTCAGCAGAGGGGTCAGTTTTCTAACTCATCTCGTCAGGACAGGC
CTCACATGAAGCCCTTTATTCTCACTCGGAATGCGGCCCAAGCCAAAGTATTTGGAGCTGGTTATCCAAGTCTGGCATCT
ATGACGGTGAATGACTGGTATGATCAGCATCGGAAATTTGGAGCATTATCAGATCAAGGAATAGTCAAGACAACATTAGA
GGTCAAAAGAGCAGCTCAGCAACAGGAAGATCAGGAAACAAAGGAGGAAGAGGATGATGAGCAAACACTGCATCAAGCTC
GGGAGTGGGATGACTGGAAGGACATCCATCCTAAAGGCTATGGTAACCGACAGAATATGGGT

ORF - retro_pvam_1462 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.55 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMAAAEDDELQLPRLPDLFESGQQLLDEVEAAAEPSGSRAVQDKVSKGLDLLKTAAEMLSQLDLFSRNEDL
MAAA..DEL.LPRLP.LFE...QLLDEVE.AAEP..SR..Q.KV.KGLDLLK.AA.MLSQLDLFS.NEDL
RetrocopyMAAAKEDELLLPRLPELFETSKQLLDEVEVAAEPISSRIIQEKVLKGLDLLKKAAKMLSQLDLFSQNEDL
ParentalEEIASSDLKYLMLPAYQGALAMKQVNPSKRLDHLQRAREHFLKYLTQCQHYRVAEFELPPKDDSAGSNAA
EEIAS.DLKYLM.PA.QGALAMKQVNPSK.LDHLQ.AREHFL.YLTQCQ.Y.VAEFELP........N..
RetrocopyEEIASTDLKYLMVPAFQGALAMKQVNPSKHLDHLQWAREHFLNYLTQCQYYHVAEFELPKTKNNSAENNT
ParentalEKSSVANPTLFAMAAQRPVKIERYKQRKEVERRLAAQKAAVESGQADDQQMRAYYLLLLRRW-VGVSLEE
..SSV....L.A...QR..KIERYKQ.KEVE.RL.A.K.AVESGQADD...R.YYLL.L.RW..G.SLEE
RetrocopyASSSVTYSSLIAITSQRQAKIERYKQKKEVEHRLSALKSAVESGQADDESIREYYLLHLQRW>IGISLEE
ParentalIESIDQEMKILREKDSPKEAAP-SSSSRQDRPPMKSFILTRNAAQAKVFGAGYPSLATMTVHDWYDQHQK
IESID.E.K.LREK.S..E....S.SSRQDRP.MK.FILTRNAAQAKVFGAGYPSLA.MTV.DWYDQH.K
RetrocopyIESIDLEIKVLREKASSAEGSV>SNSSRQDRPHMKPFILTRNAAQAKVFGAGYPSLASMTVNDWYDQHRK
ParentalVGVLPDQGLAKTSAAEVRKAARRQEEPDIEEDEEDEETLQRAREWDDWKDTHPRGYGNRQNMG
.G.L.DQG..KT...EV..AA..QE.....E.E.DE.TL..AREWDDWKD.HP.GYGNRQNMG
RetrocopyFGALSDQGIVKTT-LEVKRAAQQQEDQETKEEEDDEQTLHQAREWDDWKDIHPKGYGNRQNMG

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






RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_1462 was not experimentally validated.

Retrocopy orthology:
Pteropus vampyrus 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 19 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000077971 retrocopy
retro_btau_215,
Choloepus hoffmanni ENSCHOG000000136543 retrocopies
retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus ENSCJAG000000125256 retrocopies
retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus ENSCPOG000000107971 retrocopy
retro_cpor_44,
Dasypus novemcinctus ENSDNOG000000147315 retrocopies
retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi ENSETEG000000033971 retrocopy
retro_etel_1637,
Felis catus ENSFCAG000000296881 retrocopy
retro_fcat_23,
Homo sapiens ENSG000000892895 retrocopies
retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla ENSGGOG000000277952 retrocopies
retro_ggor_112, retro_ggor_2020,
Myotis lucifugus ENSMLUG000000041791 retrocopy
retro_mluc_316,
Macaca mulatta ENSMMUG000000139292 retrocopies
retro_mmul_1545, retro_mmul_31,
Mus musculus ENSMUSG000000312211 retrocopy
retro_mmus_169,
Nomascus leucogenys ENSNLEG000000007475 retrocopies
retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii ENSOGAG000000117971 retrocopy
retro_ogar_110,
Pongo abelii ENSPPYG000000204354 retrocopies
retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes ENSPTRG000000219905 retrocopies
retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus ENSPVAG00000005483 1 retrocopy
retro_pvam_1462 ,
Rattus norvegicus ENSRNOG000000262671 retrocopy
retro_rnor_311,
Tarsius syrichta ENSTSYG000000062142 retrocopies
retro_tsyr_1537, retro_tsyr_2131,


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