RetrogeneDB ID:

retro_nleu_278

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397262.1:21583610..21584153(-)
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:ENSNLEG00000000720
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_nleu_278
ATGGGCAAAGGAGATCCTAAAAAGCCGAGAGGCAAAATGTCATCATATGCATTTTTTTGTGCAAATTTGTCGGGAGGAGC
ATAAGAAGAAGCACCCAGATGCTTCAGTCAACTTCTCAGAGTTTTCTAAGAAGTGCTCAGAGAGGTGGAAGACCATATCT
GCTAAAGAGAAAGGAAAATTTGAGGATATGGCAAAGGCGGACAAGGCCTATTATGAAAGAGAAATGAAAACTTATATCCC
TCCCAAAGGGGAGACAAAAAAAGAAGTTCAAGGATCCCAATGCACCAAGAGGCCTCCTTCGGCCTTCTTCCTGTTCTGCT
CTGAGTATCGCCCAAAAATCAAAGGAGAACATCCTGGCCTGTCCATTGGTGATGCTGCGAAGAAACTGGGAGAGATGTGG
AATAACACTGCTGCAGCTGACAAGCAGCCTTAGGAAAAGAAGGCTGTGAAGCTGAAGGAAAAATACGAAAAGGATATTGC
TGCATATCGAGCTAAAGGAAAGCCTGATGCAGCAAAAAGGGAGTTGTCAAGGCTGAAAAAAGC

ORF - retro_nleu_278 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.05 %
Parental protein coverage: 84.19 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMGKGDPKKPRGKMSSYAFF-VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA
MGKGDPKKPRGKMSSYAFF.VQ.CREEHKKKHPDASVNFSEFSKKCSERWKT.SAKEKGKFEDMAKADKA
RetrocopyMGKGDPKKPRGKMSSYAFF>VQICREEHKKKHPDASVNFSEFSKKCSERWKTISAKEKGKFEDMAKADKA
ParentalRYEREMKTYIPPKGET-KKKFKDPNAP-KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA
.YEREMKTYIPPKGET.KKKFKDPNAP.KRPPSAFFLFCSEYRPKIKGEHPGLSIGD.AKKLGEMWNNTA
RetrocopyYYEREMKTYIPPKGET>KKKFKDPNAP<KRPPSAFFLFCSEYRPKIKGEHPGLSIGDAAKKLGEMWNNTA
ParentalADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAA-KKGVVKAEKS
A.DKQP.EKKA.KLKEKYEKDIAAYRAKGKPDAA.KKGVVKAEKS
RetrocopyAADKQP*EKKAVKLKEKYEKDIAAYRAKGKPDAA<KKGVVKAEKS

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






Nomascus leucogenys was not studied using RNA-Seq expression data.
Nomascus leucogenys was not studied using ChIP-Seq data.
Nomascus leucogenys was not studied using EST data.
Nomascus leucogenys was not studied using FANTOM5 data.
retro_nleu_278 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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 16 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 ENSNLEG00000000720 33 retrocopies
Nomascus leucogenys ENSNLEG000000066623 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sus scrofa ENSSSCG000000093273 retrocopies
Tursiops truncatus ENSTTRG000000103278 retrocopies



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