RetrogeneDB ID:

retro_ggor_1959

Retrocopy
location
Organism:Gorilla (Gorilla gorilla)
Coordinates:3:93010037..93010421(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSGGOG00000024517
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DHFR
Ensembl ID:ENSGGOG00000022366
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ggor_1959
CTAAACTGCATCGTCGCTGTGTCCCAAAACATGGGCATCGGCAAGAACGGGGACCTGCCCAGGCCGCCACTCAGGAATGA
ATTCAGGTATTTCCAGAGAATGACCACAACTTCTTCAGTAGAGGGTAAACAGAATCTGGTGATTATGGGTAGGAAGACCT
GGTTCTCCATTCCTGAGAAGAATCGACCTTTAAAGGATAGAATTAATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCA
CAAGGAGCTCATTTTCTTGCCAGAAGTTTGGATGATGCCTTAAAACTTACTGAAGGACCAGAATTAGCAAATAAAGTAGA
CATGATTTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATCACTTAAACTATTTG

ORF - retro_ggor_1959 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.19 %
Parental protein coverage: 68.45 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalLNCIVAVSQNMGIGKNGVLPWPPLRNEFRYFQRMTTTSSVEGKQNLVIMGKKTWFSIPEKNRPLKGRINL
LNCIVAVSQNMGIGKNG.LP.PPLRNEFRYFQRMTTTSSVEGKQNLVIMG.KTWFSIPEKNRPLK.RINL
RetrocopyLNCIVAVSQNMGIGKNGDLPRPPLRNEFRYFQRMTTTSSVEGKQNLVIMGRKTWFSIPEKNRPLKDRINL
ParentalVLSRELKEPPQGAHFLSRSLDDALKLTEQPELANKVDMVWIVGGSSVYKEAMNHPGHL
VLSRELKEPPQGAHFL.RSLDDALKLTE.PELANKVDM.WIVGGSSVYKEAMNH...L
RetrocopyVLSRELKEPPQGAHFLARSLDDALKLTEGPELANKVDMIWIVGGSSVYKEAMNHLNYL

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 1 .82 RPM
SRP007412_cerebellum 0 .59 RPM 2 .32 RPM
SRP007412_heart 0 .06 RPM 0 .59 RPM
SRP007412_kidney 0 .12 RPM 7 .28 RPM
SRP007412_liver 0 .03 RPM 5 .59 RPM
SRP007412_testis 0 .10 RPM 5 .91 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_1959 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ggor_1959 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_6
Pan troglodytes retro_ptro_109
Macaca mulatta retro_mmul_1496
Callithrix jacchus retro_cjac_2017
Parental genes homology:
Parental genes homology involve 19 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000157502 retrocopies
retro_amel_218, retro_amel_842,
Bos taurus ENSBTAG000000076811 retrocopy
retro_btau_351,
Callithrix jacchus ENSCJAG000000195564 retrocopies
retro_cjac_2017, retro_cjac_2298, retro_cjac_2446, retro_cjac_531,
Equus caballus ENSECAG000000268271 retrocopy
retro_ecab_513,
Felis catus ENSFCAG000000267453 retrocopies
retro_fcat_579, retro_fcat_705, retro_fcat_841,
Homo sapiens ENSG000002287164 retrocopies
retro_hsap_1927, retro_hsap_2119, retro_hsap_3602, retro_hsap_6,
Gorilla gorilla ENSGGOG00000022366 2 retrocopies
retro_ggor_1959 , retro_ggor_2429,
Myotis lucifugus ENSMLUG000000122002 retrocopies
retro_mluc_1109, retro_mluc_2577,
Macaca mulatta ENSMMUG0000001828313 retrocopies
retro_mmul_1496, retro_mmul_425, retro_mmul_692, retro_mmul_693, retro_mmul_695, retro_mmul_700, retro_mmul_701, retro_mmul_704, retro_mmul_738, retro_mmul_760, retro_mmul_768, retro_mmul_82, retro_mmul_994,
Monodelphis domestica ENSMODG000000248603 retrocopies
retro_mdom_1685, retro_mdom_604, retro_mdom_703,
Mustela putorius furoENSMPUG000000087041 retrocopy
retro_mputfur_1107,
Mus musculus ENSMUSG000000217071 retrocopy
retro_mmus_3326,
Nomascus leucogenys ENSNLEG000000129893 retrocopies
retro_nleu_1193, retro_nleu_2314, retro_nleu_2631,
Oryctolagus cuniculus ENSOCUG000000051273 retrocopies
retro_ocun_1351, retro_ocun_1640, retro_ocun_650,
Otolemur garnettii ENSOGAG000000253201 retrocopy
retro_ogar_222,
Pongo abelii ENSPPYG000000156002 retrocopies
retro_pabe_2959, retro_pabe_41,
Pan troglodytes ENSPTRG000000170423 retrocopies
retro_ptro_109, retro_ptro_1551, retro_ptro_2988,
Rattus norvegicus ENSRNOG000000135211 retrocopy
retro_rnor_2030,
Sus scrofa ENSSSCG000000141252 retrocopies
retro_sscr_104, retro_sscr_1131,


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