RetrogeneDB ID:

retro_pvam_194

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_180:408931..409416(+)
Located in intron of:ENSPVAG00000017047
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GCSH
Ensembl ID:ENSPVAG00000009956
Aliases:None
Description:glycine cleavage system protein H (aminomethyl carrier) [Source:HGNC Symbol;Acc:4208]


Retrocopy-Parental alignment summary:






>retro_pvam_194
CAAGCCTATGCCTGCAGAATACCACAGGCTTCTGTGTCCATCTGCCTTGACTGTATGTAACCCTGGGGGCTAAGGGTGGG
CGCTGTCCAGAAACTGGGCACCGGCCCCCCTCTGCTCTTGGTGTGTAAATTCACAGATAAACATTAATGGGCAACAACAA
AAAATGTGACTGGAAGAACAGGGAACAGCAGTTTTGCACAGAAAGCTTTGGGAGATGTGGTTTACTGTTTCCCTGAAGCT
GGAACAAAATTGAACAAATAAGATAAGTTTGGTGCTTTGGAAAATGTGAAACCTGTTAGTGAACTCTTATTCTCCTCTAT
CAGAAGTTAAATGAAATTAATTAAGCTCTTGCATAAAATCCAAGACTTGTCAACAATTCTTGTTATGAAGATACATGACT
GATCAAAATGATACTGAGTAATCTCTCAGAACTAGATAAACTAATGAATGAAAAAGCATGTGAGAAATACATAAACTCTA
TTGAG

ORF - retro_pvam_194 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.03 %
Parental protein coverage: 94.22 %
Number of stop codons detected: 6
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalRAVACSLRAASAPAAPCAPRFWGLRAGAIRTLRTGPNLLSVRKFTEKHEWITTENGIGTVGISNFAQEAL
.A.AC....AS..........WGLR.GA...L.TGP.LL.V.KFT.KH.W.TT.N..G..G.S.FAQ.AL
RetrocopyQAYACRIPQASVSICLDCM*PWGLRVGAVQKLGTGPPLLLVCKFTDKH*WATTKNVTGRTGNSSFAQKAL
ParentalGDVVYCSLPEVGTKLNKQDEFGALESVKAASEL-YSPLSGEV-TEINEALAENPGLVNKSCYDDGWLIKM
GDVVYC..PE.GTKLNK.D.FGALE.VK..SEL.YSPLS.EV..EIN.ALA.NP.LVN.SCY.D..LIKM
RetrocopyGDVVYC-FPEAGTKLNK*DKFGALENVKPVSEL>YSPLS-EV>NEIN*ALA*NPRLVNNSCYEDT*LIKM
ParentalTLSNPSELDELMSEEAYEKYIKSIE
.LSN.SELD.LM.E.A.EKYI.SIE
RetrocopyILSNLSELDKLMNEKACEKYINSIE

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_194 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 23 parental genes, and 168 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000089051 retrocopy
retro_acar_75,
Ailuropoda melanoleuca ENSAMEG000000139595 retrocopies
retro_amel_1362, retro_amel_1877, retro_amel_229, retro_amel_432, retro_amel_80,
Bos taurus ENSBTAG000000067958 retrocopies
retro_btau_1128, retro_btau_12, retro_btau_1483, retro_btau_1543, retro_btau_1628, retro_btau_246, retro_btau_265, retro_btau_94,
Canis familiaris ENSCAFG000000200145 retrocopies
retro_cfam_1249, retro_cfam_1543, retro_cfam_358, retro_cfam_618, retro_cfam_732,
Choloepus hoffmanni ENSCHOG0000000243437 retrocopies
retro_chof_1011, retro_chof_1019, retro_chof_1123, retro_chof_1213, retro_chof_1324, retro_chof_1410, retro_chof_1482, retro_chof_1550, retro_chof_163, retro_chof_1647, retro_chof_1659, retro_chof_1690, retro_chof_1705, retro_chof_1722, retro_chof_178, retro_chof_1781, retro_chof_1787, retro_chof_219, retro_chof_2264, retro_chof_2289, retro_chof_2319, retro_chof_2412, retro_chof_2466, retro_chof_2494, retro_chof_2632, retro_chof_2657, retro_chof_283, retro_chof_335, retro_chof_361, retro_chof_362, retro_chof_363, retro_chof_419, retro_chof_433, retro_chof_477, retro_chof_597, retro_chof_755, retro_chof_931,
Callithrix jacchus ENSCJAG000000166548 retrocopies
retro_cjac_1071, retro_cjac_1576, retro_cjac_1674, retro_cjac_1804, retro_cjac_2650, retro_cjac_3280, retro_cjac_3470, retro_cjac_552,
Cavia porcellus ENSCPOG000000099833 retrocopies
retro_cpor_1240, retro_cpor_385, retro_cpor_463,
Dipodomys ordii ENSDORG000000078311 retrocopy
retro_dord_645,
Felis catus ENSFCAG000000130388 retrocopies
retro_fcat_1007, retro_fcat_1112, retro_fcat_1294, retro_fcat_1435, retro_fcat_1627, retro_fcat_1920, retro_fcat_215, retro_fcat_354,
Loxodonta africana ENSLAFG000000155863 retrocopies
retro_lafr_554, retro_lafr_822, retro_lafr_900,
Myotis lucifugus ENSMLUG0000000578312 retrocopies
retro_mluc_1151, retro_mluc_1221, retro_mluc_1466, retro_mluc_1538, retro_mluc_1659, retro_mluc_1685, retro_mluc_2089, retro_mluc_2090, retro_mluc_2139, retro_mluc_2314, retro_mluc_2411, retro_mluc_709,
Macaca mulatta ENSMMUG000000130885 retrocopies
retro_mmul_1192, retro_mmul_2202, retro_mmul_661, retro_mmul_840, retro_mmul_960,
Mustela putorius furoENSMPUG000000096774 retrocopies
retro_mputfur_1434, retro_mputfur_1492, retro_mputfur_349, retro_mputfur_809,
Mus musculus ENSMUSG000000344248 retrocopies
retro_mmus_1880, retro_mmus_2144, retro_mmus_2235, retro_mmus_3062, retro_mmus_3303, retro_mmus_3459, retro_mmus_3610, retro_mmus_3703,
Nomascus leucogenys ENSNLEG000000268441 retrocopy
retro_nleu_365,
Ochotona princeps ENSOPRG000000032811 retrocopy
retro_opri_790,
Procavia capensis ENSPCAG000000058201 retrocopy
retro_pcap_207,
Pteropus vampyrus ENSPVAG00000009956 8 retrocopies
retro_pvam_1253, retro_pvam_1474, retro_pvam_1481, retro_pvam_194 , retro_pvam_552, retro_pvam_583, retro_pvam_78, retro_pvam_958,
Rattus norvegicus ENSRNOG000000115356 retrocopies
retro_rnor_1217, retro_rnor_1218, retro_rnor_1400, retro_rnor_1910, retro_rnor_2691, retro_rnor_557,
Sarcophilus harrisii ENSSHAG000000055291 retrocopy
retro_shar_239,
Ictidomys tridecemlineatus ENSSTOG000000164332 retrocopies
retro_itri_31, retro_itri_34,
Tupaia belangeri ENSTBEG0000000005627 retrocopies
retro_tbel_1426, retro_tbel_1716, retro_tbel_1766, retro_tbel_1846, retro_tbel_1923, retro_tbel_2026, retro_tbel_2074, retro_tbel_2168, retro_tbel_2315, retro_tbel_2426, retro_tbel_2489, retro_tbel_2515, retro_tbel_2573, retro_tbel_2769, retro_tbel_3007, retro_tbel_3025, retro_tbel_311, retro_tbel_3140, retro_tbel_3458, retro_tbel_3852, retro_tbel_3924, retro_tbel_4173, retro_tbel_4727, retro_tbel_597, retro_tbel_601, retro_tbel_609, retro_tbel_825,
Tarsius syrichta ENSTSYG0000000024813 retrocopies
retro_tsyr_119, retro_tsyr_1311, retro_tsyr_1367, retro_tsyr_1833, retro_tsyr_2023, retro_tsyr_2173, retro_tsyr_309, retro_tsyr_328, retro_tsyr_363, retro_tsyr_429, retro_tsyr_439, retro_tsyr_587, retro_tsyr_643,


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