RetrogeneDB ID:

retro_pvam_356

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:GeneScaffold_2704:501752..502166(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB3
Ensembl ID:ENSPVAG00000000219
Aliases:None
Description:high mobility group box 3 [Source:HGNC Symbol;Acc:5004]


Retrocopy-Parental alignment summary:






>retro_pvam_356
ATGGGCAAAGGAGATTCCTAAAAAGCCACGAGGCGAAATGTCATCATATGCATTCTTTGTGAAAACTCACCGGGAGGAGC
AAAAGAAGAAGCAACTGGATGCTTCAGTCAACTCCTCAGAGTTTTCTAAGAAGTGCTCAGAGAAGTAGAAGACCAGGTAT
GCTAAAGAGAAAGGAAAATTTGAAGACATGGCAAAGGCGGACGAGGCCCACTATGAAAGAGAAATGAAAACTTACATTCC
TCCTAAAGGGGAAGCAAAGAGAATCCCAATGCATCCGAGGGGTCTCCTTCGTTCTTTTTCTTGTTTTGTTCTCAGCATCG
CCCAAAAATCAAAGGAGAGCATCCTGGCCTATCCATTGGTGATGTTGCAAAGAAGCTGGGAGAGATGTGTAATAACACTG
CTGCAGGTGACAAA

ORF - retro_pvam_356 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.12 %
Parental protein coverage: 69.85 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAKGD-PKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKV
M.KGD.PKKP.G.MS.YAFFV.T.REE.KKK.....VN..EFSKKCSE..KT...KEK.KF..MAKAD..
RetrocopyMGKGD>PKKPRGEMSSYAFFVKTHREEQKKKQLDASVNSSEFSKKCSEK*KTRYAKEKGKFEDMAKADEA
ParentalRYDREMKDYGPAKG-GKKKKDPNAPKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLSDSE
.Y.REMK.Y.P.KG.G.K...PNA....PS.FFLFCS..RPKIK...PG.SIGDVAKKLGEM.NN.....
RetrocopyHYEREMKTYIPPKG<GSK-ENPNASEGSPSFFFLFCSQHRPKIKGEHPGLSIGDVAKKLGEMCNNTAAGD
ParentalK
K
RetrocopyK

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_356 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 34 parental genes, and 213 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000051502 retrocopies
retro_btau_190, retro_btau_38,
Canis familiaris ENSCAFG000000287151 retrocopy
retro_cfam_1537,
Choloepus hoffmanni ENSCHOG000000050052 retrocopies
retro_chof_1891, retro_chof_2010,
Callithrix jacchus ENSCJAG000000039369 retrocopies
retro_cjac_1596, retro_cjac_1950, retro_cjac_2343, retro_cjac_2469, retro_cjac_2470, retro_cjac_2738, retro_cjac_2900, retro_cjac_688, retro_cjac_965,
Cavia porcellus ENSCPOG000000006012 retrocopies
retro_cpor_1432, retro_cpor_384,
Dipodomys ordii ENSDORG000000108264 retrocopies
retro_dord_214, retro_dord_337, retro_dord_454, retro_dord_609,
Equus caballus ENSECAG000000205961 retrocopy
retro_ecab_890,
Echinops telfairi ENSETEG000000156894 retrocopies
retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
Felis catus ENSFCAG000000246244 retrocopies
retro_fcat_1480, retro_fcat_1504, retro_fcat_265, retro_fcat_865,
Homo sapiens ENSG000000299938 retrocopies
retro_hsap_1461, retro_hsap_1873, retro_hsap_2621, retro_hsap_3064, retro_hsap_3683, retro_hsap_4251, retro_hsap_4904, retro_hsap_627,
Gorilla gorilla ENSGGOG0000002716416 retrocopies
retro_ggor_1371, retro_ggor_1538, retro_ggor_1540, retro_ggor_1651, retro_ggor_1834, retro_ggor_2104, retro_ggor_2250, retro_ggor_2469, retro_ggor_2490, retro_ggor_2580, retro_ggor_272, retro_ggor_2944, retro_ggor_301, retro_ggor_414, retro_ggor_549, retro_ggor_618,
Loxodonta africana ENSLAFG000000258771 retrocopy
retro_lafr_893,
Microcebus murinus ENSMICG000000156684 retrocopies
retro_mmur_564, retro_mmur_60, retro_mmur_853, retro_mmur_994,
Myotis lucifugus ENSMLUG000000109264 retrocopies
retro_mluc_1055, retro_mluc_1989, retro_mluc_215, retro_mluc_529,
Macaca mulatta ENSMMUG0000000463320 retrocopies
retro_mmul_1003, retro_mmul_1115, retro_mmul_1143, retro_mmul_1303, retro_mmul_1341, retro_mmul_1482, retro_mmul_1568, retro_mmul_1624, retro_mmul_1799, retro_mmul_1957, retro_mmul_2106, retro_mmul_2425, retro_mmul_2451, retro_mmul_2469, retro_mmul_2484, retro_mmul_2526, retro_mmul_267, retro_mmul_399, retro_mmul_514, retro_mmul_597,
Monodelphis domestica ENSMODG000000057357 retrocopies
retro_mdom_1257, retro_mdom_1508, retro_mdom_1883, retro_mdom_1952, retro_mdom_587, retro_mdom_698, retro_mdom_831,
Mustela putorius furoENSMPUG000000116062 retrocopies
retro_mputfur_138, retro_mputfur_26,
Mus musculus ENSMUSG000000152171 retrocopy
retro_mmus_273,
Oryctolagus cuniculus ENSOCUG000000059867 retrocopies
retro_ocun_1033, retro_ocun_1913, retro_ocun_1914, retro_ocun_534, retro_ocun_568, retro_ocun_891, retro_ocun_931,
Otolemur garnettii ENSOGAG0000000177319 retrocopies
retro_ogar_1318, retro_ogar_1647, retro_ogar_1728, retro_ogar_187, retro_ogar_1930, retro_ogar_204, retro_ogar_2076, retro_ogar_2530, retro_ogar_2591, retro_ogar_2678, retro_ogar_2743, retro_ogar_2983, retro_ogar_3127, retro_ogar_3371, retro_ogar_343, retro_ogar_3433, retro_ogar_3479, retro_ogar_3513, retro_ogar_65,
Procavia capensis ENSPCAG000000019451 retrocopy
retro_pcap_328,
Pongo abelii ENSPPYG0000002081822 retrocopies
retro_pabe_1207, retro_pabe_1411, retro_pabe_1505, retro_pabe_1580, retro_pabe_1823, retro_pabe_1825, retro_pabe_1927, retro_pabe_2339, retro_pabe_2538, retro_pabe_2712, retro_pabe_2816, retro_pabe_3000, retro_pabe_3041, retro_pabe_3144, retro_pabe_3387, retro_pabe_3685, retro_pabe_3813, retro_pabe_410, retro_pabe_442, retro_pabe_560, retro_pabe_632, retro_pabe_784,
Pan troglodytes ENSPTRG0000002237122 retrocopies
retro_ptro_1115, retro_ptro_1211, retro_ptro_1276, retro_ptro_1429, retro_ptro_1432, retro_ptro_1561, retro_ptro_174, retro_ptro_1766, retro_ptro_2066, retro_ptro_213, retro_ptro_2218, retro_ptro_2296, retro_ptro_2477, retro_ptro_2497, retro_ptro_2608, retro_ptro_2891, retro_ptro_2944, retro_ptro_3154, retro_ptro_3271, retro_ptro_456, retro_ptro_522, retro_ptro_629,
Pteropus vampyrus ENSPVAG00000000219 1 retrocopy
retro_pvam_356 ,
Pteropus vampyrus ENSPVAG000000014316 retrocopies
retro_pvam_1156, retro_pvam_154, retro_pvam_429, retro_pvam_508, retro_pvam_774, retro_pvam_960,
Pteropus vampyrus ENSPVAG000000146561 retrocopy
retro_pvam_872,
Rattus norvegicus ENSRNOG000000110964 retrocopies
retro_rnor_1049, retro_rnor_2303, retro_rnor_2359, retro_rnor_2363,
Rattus norvegicus ENSRNOG000000509105 retrocopies
retro_rnor_1956, retro_rnor_2516, retro_rnor_2625, retro_rnor_720, retro_rnor_954,
Sarcophilus harrisii ENSSHAG000000029162 retrocopies
retro_shar_139, retro_shar_316,
Sus scrofa ENSSSCG000000127453 retrocopies
retro_sscr_1094, retro_sscr_466, retro_sscr_467,
Ictidomys tridecemlineatus ENSSTOG000000239086 retrocopies
retro_itri_1366, retro_itri_1527, retro_itri_1655, retro_itri_1749, retro_itri_777, retro_itri_909,
Tupaia belangeri ENSTBEG0000000306818 retrocopies
retro_tbel_1002, retro_tbel_1230, retro_tbel_1579, retro_tbel_1700, retro_tbel_1819, retro_tbel_2543, retro_tbel_2730, retro_tbel_3261, retro_tbel_3476, retro_tbel_3623, retro_tbel_3781, retro_tbel_408, retro_tbel_410, retro_tbel_4203, retro_tbel_4209, retro_tbel_4299, retro_tbel_605, retro_tbel_698,
Tursiops truncatus ENSTTRG000000002052 retrocopies
retro_ttru_1187, retro_ttru_372,
Vicugna pacos ENSVPAG000000000962 retrocopies
retro_vpac_245, retro_vpac_434,


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