RetrogeneDB ID:

retro_ogar_3323

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873778.1:1257163..1257663(-)
Located in intron of:ENSOGAG00000030896
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB2
Ensembl ID:ENSOGAG00000017149
Aliases:None
Description:high mobility group box 2 [Source:HGNC Symbol;Acc:5000]


Retrocopy-Parental alignment summary:






>retro_ogar_3323
ATGGGTAAAGGAGATCCAAAAAGCCGAGAGGCAAAATGTCATCACATGCATTCTTTGTGCAAACTTGTTTGTTGGGAGGA
GCACACGAAGCACTCAGATGCTTCAGTCAACTTCTCAGAGTTTTCTAAGAAGTGCTCAGACAGGTGGAAGACCATGTCTG
ATAAAGAGAAAGGAAAATCTGAAGATATGGCAAAGGCAGGTAAGGCCCGTTATGAAAGAGAAAACCTATATCCCTCCTAA
AGGGGAAACAAAAAAGAAGTTCAAGGATCCCAATGCACCCAAGAGGCCTCCTTCGGTCTTTTTCTTGTTCTGTTCTGAGT
ATCACCCCAAAATCAAAAGAGAACATCCCAGCCTATCCATTTGATGATGTTACAAAGAATGTGGGAGAGATGTAGAATAC
TGTAGATGACAAGCAACTTAATGAAAAGAAGGCTGCAAAGCTGGAGGATAAATATGAAAAGGATATTGCTACATACTGAG
CTAAAAGAAAGTGTGATGCA

ORF - retro_ogar_3323 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.82 %
Parental protein coverage: 81.34 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPN-KPRGKMSSYAFFVQTCR-EEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKNDK
MGKGDP..KPRGKMSS.AFFVQTC...E...KH.D.SVNF.EFSKKCS.RWKTMS.KEK.K.EDMAK..K
RetrocopyMGKGDPK<KPRGKMSSHAFFVQTCL>WEEHTKHSDASVNFSEFSKKCSDRWKTMSDKEKGKSEDMAKAGK
ParentalARYDREMKNYVP-PKGDKKGKKKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGLSI-GDTAKKLGEMWSEQ
ARY.RE..N..P.PKG..K.K.KDPNAPKRPPS.FFLFCSE..PKIK.EHP.LSI..D..K..GEM....
RetrocopyARYERE--NLYP>PKGETKKKFKDPNAPKRPPSVFFLFCSEYHPKIKREHPSLSI>DDVTKNVGEM*N--
ParentalSAKDKQPYEQKAAKLKEKYEKDIAAYRAKGKSEA
...DKQ..E.KAAKL..KYEKDIA.Y.AK.K..A
RetrocopyTVDDKQLNEKKAAKLEDKYEKDIATY*AKRKCDA

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_3323 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 18 parental genes, and 158 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000151011 retrocopy
retro_btau_58,
Dasypus novemcinctus ENSDNOG000000194404 retrocopies
retro_dnov_1142, retro_dnov_1457, retro_dnov_454, retro_dnov_532,
Echinops telfairi ENSETEG000000103793 retrocopies
retro_etel_1474, retro_etel_1841, retro_etel_2023,
Echinops telfairi ENSETEG000000163791 retrocopy
retro_etel_414,
Felis catus ENSFCAG000000042182 retrocopies
retro_fcat_279, retro_fcat_52,
Homo sapiens ENSG000001641041 retrocopy
retro_hsap_3663,
Gorilla gorilla ENSGGOG000000158821 retrocopy
retro_ggor_2474,
Macropus eugenii ENSMEUG000000022563 retrocopies
retro_meug_1920, retro_meug_1989, retro_meug_550,
Monodelphis domestica ENSMODG000000035273 retrocopies
retro_mdom_1160, retro_mdom_1919, retro_mdom_69,
Nomascus leucogenys ENSNLEG000000066623 retrocopies
retro_nleu_113, retro_nleu_517, retro_nleu_550,
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,
Otolemur garnettii ENSOGAG00000003205104 retrocopies
retro_ogar_1008, retro_ogar_1043, retro_ogar_106, retro_ogar_1133, retro_ogar_123, retro_ogar_1232, retro_ogar_1296, retro_ogar_1299, retro_ogar_1330, retro_ogar_1386, retro_ogar_1398, retro_ogar_1399, retro_ogar_1421, retro_ogar_1423, retro_ogar_1424, retro_ogar_1431, retro_ogar_1461, retro_ogar_1560, retro_ogar_1571, retro_ogar_1585, retro_ogar_1597, retro_ogar_1600, retro_ogar_1607, retro_ogar_1628, retro_ogar_163, retro_ogar_1664, retro_ogar_1698, retro_ogar_17, retro_ogar_172, retro_ogar_1738, retro_ogar_1758, retro_ogar_1781, retro_ogar_1843, retro_ogar_1844, retro_ogar_1861, retro_ogar_1867, retro_ogar_1878, retro_ogar_1894, retro_ogar_1896, retro_ogar_198, retro_ogar_1991, retro_ogar_2136, retro_ogar_2165, retro_ogar_219, retro_ogar_2282, retro_ogar_2318, retro_ogar_2319, retro_ogar_2352, retro_ogar_2385, retro_ogar_2403, retro_ogar_2429, retro_ogar_2436, retro_ogar_2458, retro_ogar_250, retro_ogar_2559, retro_ogar_2598, retro_ogar_2615, retro_ogar_2618, retro_ogar_2730, retro_ogar_2777, retro_ogar_2778, retro_ogar_2814, retro_ogar_2824, retro_ogar_2836, retro_ogar_284, retro_ogar_2845, retro_ogar_2891, retro_ogar_2894, retro_ogar_2906, retro_ogar_2961, retro_ogar_3008, retro_ogar_3018, retro_ogar_3028, retro_ogar_304, retro_ogar_311, retro_ogar_3136, retro_ogar_317, retro_ogar_320, retro_ogar_3208, retro_ogar_3230, retro_ogar_3325, retro_ogar_3330, retro_ogar_3355, retro_ogar_3374, retro_ogar_3500, retro_ogar_422, retro_ogar_435, retro_ogar_511, retro_ogar_542, retro_ogar_547, retro_ogar_634, retro_ogar_663, retro_ogar_698, retro_ogar_716, retro_ogar_772, retro_ogar_778, retro_ogar_8, retro_ogar_835, retro_ogar_890, retro_ogar_904, retro_ogar_912, retro_ogar_918, retro_ogar_92, retro_ogar_933,
Otolemur garnettii ENSOGAG00000017149 3 retrocopies
retro_ogar_3117, retro_ogar_3323 , retro_ogar_3336,
Otolemur garnettii ENSOGAG000000321471 retrocopy
retro_ogar_1712,
Pongo abelii ENSPPYG000000152043 retrocopies
retro_pabe_297, retro_pabe_3005, retro_pabe_3380,
Pan troglodytes ENSPTRG000000165973 retrocopies
retro_ptro_19, retro_ptro_2484, retro_ptro_2789,
Rattus norvegicus ENSRNOG000000131672 retrocopies
retro_rnor_173, retro_rnor_54,
Tursiops truncatus ENSTTRG000000156501 retrocopy
retro_ttru_1640,


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