RetrogeneDB ID:

retro_ggor_1014

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:13:82187957..82188341(-)
Located in intron of:ENSGGOG00000034999
Retrocopy
information
Ensembl ID:ENSGGOG00000027760
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H2AFZ
Ensembl ID:ENSGGOG00000027801
Aliases:None
Description:Histone H2A [Source:UniProtKB/TrEMBL;Acc:G3SDI3]


Retrocopy-Parental alignment summary:






>retro_ggor_1014
ATGGCTGGCGGTAAGGCTGGGAAGGACTCTGGAAAGGCCAAGACAAAGGCGGTTTCCCGCTCGCAGAGAGCCGGCTTGCA
GTTCCCAGTGGGCTGTATTCATCAACACCTGAAATCCAGGACGATGGGTAACAGACATGTGGGTGCAACTGCCGCTGTGT
ACAGCACAGCCATCCTGGAGTACCTCACCGCAGAGGGACTTGAACTGGCAGGAAATGCATCAAAAGACTTAAAGGTAAAG
TGTATATTACCCCTCGTCACTTGCAACTTGCTATTCGTGCAGATGAAGAATTGGATTCTCATCAAGGCTACAATTGCTGG
TGGTGGTGTCATTCCACACATCCACAAATCTCTGATTGGGAAGAAAGGACAACAGAAGACTGTC

ORF - retro_ggor_1014 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.44 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELA
MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVG.IH.HLKSRT.....VGATAAVYS.AILEYLTAE.LELA
RetrocopyMAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGCIHQHLKSRTMGNRHVGATAAVYSTAILEYLTAEGLELA
ParentalGNASKD-LKVK-RITPRHLQLAIRGDEELDS-LIKATIAGGGVIPHIHKSLIGKKGQQKTV
GNASKD.LK.K..ITPRHLQLAIR.DEELDS........GG.VIPHIHKSLIGKKGQQKTV
RetrocopyGNASKD<LKGKVYITPRHLQLAIRADEELDS>IKATIAGGG-VIPHIHKSLIGKKGQQKTV

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






RNA-Seq - click to see more details

(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
SRP007412_brain_prefrontal_cortex 0 .10 RPM 54 .24 RPM
SRP007412_cerebellum 0 .00 RPM 35 .30 RPM
SRP007412_heart 0 .00 RPM 10 .19 RPM
SRP007412_kidney 0 .12 RPM 26 .54 RPM
SRP007412_liver 0 .05 RPM 19 .84 RPM
SRP007412_testis 0 .10 RPM 87 .02 RPM

ChIP-Seq - click to see more details

Gorilla gorilla was not studied using ChIP-Seq data.

EST - click to see more details

Gorilla gorilla was not studied using EST data.

TSS - click to see more details

Gorilla gorilla was not studied using FANTOM5 data.

Lab - click to see more details

retro_ggor_1014 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_1014 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1292
Pan troglodytes retro_ptro_884
Pongo abelii retro_pabe_1070
Macaca mulatta retro_mmul_1320
Parental genes homology:
Parental genes homology involve 23 parental genes, and 96 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009591 retrocopy
retro_amel_1183,
Canis familiaris ENSCAFG000000106152 retrocopies
retro_cfam_1000, retro_cfam_101,
Callithrix jacchus ENSCJAG000000152351 retrocopy
retro_cjac_91,
Echinops telfairi ENSETEG000000066132 retrocopies
retro_etel_137, retro_etel_54,
Homo sapiens ENSG000001640326 retrocopies
retro_hsap_1292, retro_hsap_2534, retro_hsap_2581, retro_hsap_4073, retro_hsap_4113, retro_hsap_598,
Gorilla gorilla ENSGGOG00000027801 6 retrocopies
retro_ggor_1014 , retro_ggor_137, retro_ggor_1616, retro_ggor_183, retro_ggor_2760, retro_ggor_720,
Loxodonta africana ENSLAFG000000284602 retrocopies
retro_lafr_1255, retro_lafr_269,
Macropus eugenii ENSMEUG000000136991 retrocopy
retro_meug_1457,
Microcebus murinus ENSMICG000000024693 retrocopies
retro_mmur_1056, retro_mmur_1159, retro_mmur_634,
Macaca mulatta ENSMMUG000000068347 retrocopies
retro_mmul_1049, retro_mmul_1320, retro_mmul_1593, retro_mmul_2368, retro_mmul_2448, retro_mmul_2465, retro_mmul_645,
Monodelphis domestica ENSMODG000000206862 retrocopies
retro_mdom_1506, retro_mdom_977,
Mustela putorius furoENSMPUG000000095192 retrocopies
retro_mputfur_1343, retro_mputfur_1529,
Mus musculus ENSMUSG000000378946 retrocopies
retro_mmus_2397, retro_mmus_2780, retro_mmus_2976, retro_mmus_3039, retro_mmus_3585, retro_mmus_953,
Nomascus leucogenys ENSNLEG000000136623 retrocopies
retro_nleu_2505, retro_nleu_2737, retro_nleu_2864,
Oryctolagus cuniculus ENSOCUG000000018882 retrocopies
retro_ocun_513, retro_ocun_728,
Otolemur garnettii ENSOGAG000000034198 retrocopies
retro_ogar_2276, retro_ogar_2377, retro_ogar_2722, retro_ogar_3255, retro_ogar_3396, retro_ogar_755, retro_ogar_866, retro_ogar_885,
Ochotona princeps ENSOPRG000000125821 retrocopy
retro_opri_404,
Pongo abelii ENSPPYG000000149577 retrocopies
retro_pabe_1070, retro_pabe_1901, retro_pabe_2374, retro_pabe_3343, retro_pabe_3367, retro_pabe_592, retro_pabe_668,
Pan troglodytes ENSPTRG000000163127 retrocopies
retro_ptro_1477, retro_ptro_1508, retro_ptro_2760, retro_ptro_2792, retro_ptro_441, retro_ptro_614, retro_ptro_884,
Rattus norvegicus ENSRNOG000000103069 retrocopies
retro_rnor_1136, retro_rnor_1202, retro_rnor_1605, retro_rnor_1933, retro_rnor_2155, retro_rnor_2413, retro_rnor_2494, retro_rnor_2908, retro_rnor_788,
Ictidomys tridecemlineatus ENSSTOG000000231941 retrocopy
retro_itri_1524,
Tupaia belangeri ENSTBEG0000000047815 retrocopies
retro_tbel_1289, retro_tbel_1290, retro_tbel_1320, retro_tbel_1925, retro_tbel_1959, retro_tbel_1972, retro_tbel_2304, retro_tbel_2526, retro_tbel_2685, retro_tbel_3575, retro_tbel_4077, retro_tbel_4308, retro_tbel_4369, retro_tbel_4451, retro_tbel_819,
Tarsius syrichta ENSTSYG000000094622 retrocopies
retro_tsyr_1715, retro_tsyr_971,


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