RetrogeneDB ID:

retro_cjac_718

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:10:92825877..92826268(+)
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:ENSCJAG00000021615
Aliases:LOC100392312, HMG-1, HMGB1
Description:High mobility group protein B1 [Source:UniProtKB/Swiss-Prot;Acc:B0CM99]


Retrocopy-Parental alignment summary:






>retro_cjac_718
GCAGACAAGGCCCATTATGAAAGAGAAATGAAAACATATATCCCTCCTAAAGGGGAGAAAAAAAAGAAGTTCAAGGATCC
CAATGCACCCAAGAGGCCTCCTTCAGCCTTTTTCTTGTTCTGTTCTGCATATGGCCCAAAAATCAAAGGAGAACATCCTG
GCCTGTCCATTGGTGATGCTGCGAAGAAGCTGGGAGGGGTGTGGAATAACACTCCTGCAGATGACAAGCAGCCTTATGAA
AAGGCTGTAAAGCTGAAGGAAAAATACAGAAAGGATATTACTGCATATTGAGCTAAAGGAAAGCCTGATGCAGCAAAAAA
GGGAGTTGTTGAGGCTGAAAAAATCGAGAAAAAAGAAGAGAAGAGGACGAGGAGAGGAAGATGAAGAAGAT

ORF - retro_cjac_718 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.09 %
Parental protein coverage: 60.93 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalADKARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNN
ADKA.YEREMKTYIPPKGE.KKKFKDPNAPKRPPSAFFLFCS.Y.PKIKGEHPGLSIGD.AKKLG..WNN
RetrocopyADKAHYEREMKTYIPPKGEKKKKFKDPNAPKRPPSAFFLFCSAYGPKIKGEHPGLSIGDAAKKLGGVWNN
ParentalTAADDKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAE-KSKKKKEEEEDEEDEED
T.ADDKQPYE.KA.KLKEKY.KDI.AY.AKGKPDAAKKGVV.AE.KS.KKK.....EEDEED
RetrocopyTPADDKQPYE-KAVKLKEKYRKDITAY*AKGKPDAAKKGVVEAE>KSRKKKRRGRGEEDEED

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






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP051959_colon 0 .40 RPM 50 .12 RPM
SRP051959_heart 0 .02 RPM 41 .15 RPM
SRP051959_kidney 0 .07 RPM 49 .70 RPM
SRP051959_liver 0 .00 RPM 35 .72 RPM
SRP051959_lung 0 .02 RPM 50 .20 RPM
SRP051959_lymph_node 0 .00 RPM 40 .20 RPM
SRP051959_skeletal_muscle 0 .00 RPM 30 .38 RPM
SRP051959_spleen 0 .08 RPM 49 .62 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_718 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_718 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_718 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1357
Gorilla gorilla retro_ggor_1057
Pongo abelii retro_pabe_1125

Parental genes homology:
Parental genes homology involve 23 parental genes, and 342 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000088807 retrocopies
Bos taurus ENSBTAG000000181032 retrocopies
Canis familiaris ENSCAFG0000000659713 retrocopies
Choloepus hoffmanni ENSCHOG0000000242316 retrocopies
Callithrix jacchus ENSCJAG000000039369 retrocopies
Callithrix jacchus ENSCJAG000000051122 retrocopies
Callithrix jacchus ENSCJAG00000021615 11 retrocopies
Cavia porcellus ENSCPOG000000039851 retrocopy
Echinops telfairi ENSETEG0000000404818 retrocopies
Homo sapiens ENSG0000018940337 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Loxodonta africana ENSLAFG000000002694 retrocopies
Macropus eugenii ENSMEUG000000013802 retrocopies
Myotis lucifugus ENSMLUG0000002597917 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Oryctolagus cuniculus ENSOCUG0000002133516 retrocopies
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,
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sarcophilus harrisii ENSSHAG000000140342 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000044319 retrocopies
Tarsius syrichta ENSTSYG000000063287 retrocopies



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