RetrogeneDB ID:

retro_ttru_1382

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_111797:210888..211410(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HMGB1
Ensembl ID:ENSTTRG00000010327
Aliases:None
Description:high mobility group box 1 [Source:HGNC Symbol;Acc:4983]


Retrocopy-Parental alignment summary:






>retro_ttru_1382
AGAAGCCAAGAGGCAAAATTTTCATTCTTTGTGCAAACTTGCTGGGAGGAACACAAGAAGCACACAGATGCTTCAGTTAG
CTTCTCAGAGTTTTCTAACAAGTGCTCAGAGAGGTGGAAGACCATGTCTGCTAAAGAAAAAAGAAAGTTTGAAGACATGG
CAGAGGCAGACAAAGCCCGTTATGAAAGAGAAATGAAAACTTATAACCCTCCTAAAAGGGAAACAAAAAAGAAGTTCAAG
GATCCCAATGCACCCAAGAGGCCTCCTTTGGCCTTTTTCTTGTTTTGTTCTGAGTATTGTCCAAAAATCAGAGGAGAACA
TCCAGGCTAATCCAGTGGTGATGTTGCAAAGAAACTGGGAGAGATGTGGAATAACACTGCTGCAGATGACAAGCAGCCTT
AGGAGAAGAAGGCTGCTAAGCTGAAGGAAAAGTACAAAAAGGATATTGCTGCATACTGAGCTAAAGGGAAGCCTGGTGCA
GCAAAAAAGGGAGTCGTCAAGGCTGAAAAAAGCAAGAAAAAG

ORF - retro_ttru_1382 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.71 %
Parental protein coverage: 81.4 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTYI
R.......FFVQTC.EEHKK.H.DASV.FSEFS.KCSERWKTMSAKEK.KFEDMA.ADKARYEREMKTY.
RetrocopyRSQEAKFSFFVQTCWEEHKK-HTDASVSFSEFSNKCSERWKTMSAKEKRKFEDMAEADKARYEREMKTYN
ParentalPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAA
PPK.ETKKKFKDPNAPKRPP.AFFLFCSEY.PKI.GEHPG.S.GDVAKKLGEMWNNTAADDKQP.EKKAA
RetrocopyPPKRETKKKFKDPNAPKRPPLAFFLFCSEYCPKIRGEHPG*SSGDVAKKLGEMWNNTAADDKQP*EKKAA
ParentalKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKK
KLKEKY.KDIAAY.AKGKP.AAKKGVVKAEKSKKK
RetrocopyKLKEKYKKDIAAY*AKGKPGAAKKGVVKAEKSKKK

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






Tursiops truncatus was not studied using RNA-Seq expression data.
Tursiops truncatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ttru_1382 retrocopy.
Tursiops truncatus was not studied using FANTOM5 data.
retro_ttru_1382 was not experimentally validated.

Retrocopy orthology:
Tursiops truncatus 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 17 parental genes, and 302 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000659713 retrocopies
Equus caballus ENSECAG000000084392 retrocopies
Felis catus ENSFCAG0000000020010 retrocopies
Homo sapiens ENSG0000018940337 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Macropus eugenii ENSMEUG000000013802 retrocopies
Microcebus murinus ENSMICG000000071447 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Mus musculus ENSMUSG00000066551129 retrocopies
retro_mmus_1025, retro_mmus_1037, retro_mmus_1047, retro_mmus_1065, retro_mmus_1094, retro_mmus_1112, retro_mmus_1113, retro_mmus_1114, retro_mmus_1115, retro_mmus_1128, retro_mmus_1135, retro_mmus_1140, retro_mmus_1178, retro_mmus_1181, retro_mmus_1209, retro_mmus_1284, retro_mmus_1302, retro_mmus_1351, retro_mmus_1407, retro_mmus_1423, retro_mmus_1508, retro_mmus_1553, retro_mmus_1554, retro_mmus_1584, retro_mmus_1672, retro_mmus_1705, retro_mmus_1706, retro_mmus_1712, retro_mmus_1716, retro_mmus_1725, retro_mmus_1775, retro_mmus_1794, retro_mmus_1800, retro_mmus_1822, retro_mmus_1845, retro_mmus_1871, retro_mmus_1989, retro_mmus_2015, retro_mmus_2077, retro_mmus_2080, retro_mmus_2096, retro_mmus_2191, retro_mmus_2194, retro_mmus_2199, retro_mmus_2209, retro_mmus_2224, retro_mmus_2229, retro_mmus_2280, retro_mmus_2300, retro_mmus_2324, retro_mmus_2404, retro_mmus_2407, retro_mmus_2409, retro_mmus_2414, retro_mmus_2420, retro_mmus_2425, retro_mmus_2467, retro_mmus_2469, retro_mmus_2524, retro_mmus_2532, retro_mmus_2627, retro_mmus_2670, retro_mmus_2682, retro_mmus_2702, retro_mmus_2719, retro_mmus_2754, retro_mmus_2789, retro_mmus_2815, retro_mmus_2823, retro_mmus_2866, retro_mmus_2877, retro_mmus_2886, retro_mmus_292, retro_mmus_2923, retro_mmus_2936, retro_mmus_2940, retro_mmus_2954, retro_mmus_2965, retro_mmus_2977, retro_mmus_303, retro_mmus_3046, retro_mmus_3056, retro_mmus_3059, retro_mmus_3067, retro_mmus_3070, retro_mmus_3075, retro_mmus_3102, retro_mmus_3106, retro_mmus_3121, retro_mmus_3169, retro_mmus_3175, retro_mmus_319, retro_mmus_3190, retro_mmus_3199, retro_mmus_3207, retro_mmus_3239, retro_mmus_3289, retro_mmus_3322, retro_mmus_3353, retro_mmus_3375, retro_mmus_3476, retro_mmus_3494, retro_mmus_3533, retro_mmus_359, retro_mmus_3612, retro_mmus_3676, retro_mmus_3692, retro_mmus_3715, retro_mmus_418, retro_mmus_515, retro_mmus_530, retro_mmus_574, retro_mmus_599, retro_mmus_618, retro_mmus_623, retro_mmus_624, retro_mmus_634, retro_mmus_704, retro_mmus_705, retro_mmus_785, retro_mmus_813, retro_mmus_839, retro_mmus_855, retro_mmus_881, retro_mmus_903, retro_mmus_906, retro_mmus_930, retro_mmus_965, retro_mmus_981,
Nomascus leucogenys ENSNLEG0000000072033 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sus scrofa ENSSSCG000000093273 retrocopies
Tursiops truncatus ENSTTRG000000002052 retrocopies
Tursiops truncatus ENSTTRG00000010327 8 retrocopies
Tursiops truncatus ENSTTRG000000156501 retrocopy



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