RetrogeneDB ID:

retro_ptro_2165

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:5:76371907..76372383(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM126A
Ensembl ID:ENSPTRG00000004134
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2165
ATGGAAAATCAGGAGCCAGATAGCACTTTCAAGGAAAAAGTAATTTTAGGCATCATAACTAGAAAAATTAACCAGCTTCC
AGAAGCAGAAAGGAAACTACTTGAACATGGATCAATATATGTTGAACTTAATGCTGTTCTCCGTGGCCTAATAGCAAACA
GTCTTTTTCTATGCATCTTGAACATGACACAGGCTCATATAGCTGCCGGCTCACCAATGGCAGAGATCCCATTTCTGATA
GTACATGTATTTTACAGAAGTTTTGTAAATTTACCTTTGAATTGAGGTCATTGGAATTTGAAACCCATACCATAAAATGA
GGTGGATTGGTTGGTCTTGTGTTTGGTGGTCTTTTCTTGACTATACCTATGAATGGTGGCTTAGAAGCCAGATATGAATC
AACTCTGTTATCAGAGAAAGGAAACATCTTAAGTTACTGGATTAGAATTTCTAAGCCTGACTTTAGAAAGATGTTG

ORF - retro_ptro_2165 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.42 %
Parental protein coverage: 82.05 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMENHKSNN--KENITIVDISRKINQLPEAERNLLENGSVYVGLNAALCGLIANSLFRRILNVTKARIAAG
MEN.......KE......I.RKINQLPEAER.LLE.GS.YV.LNA.L.GLIANSLF..ILN.T.A.IAAG
RetrocopyMENQEPDSTFKEKVILGIITRKINQLPEAERKLLEHGSIYVELNAVLRGLIANSLFLCILNMTQAHIAAG
ParentalLPMAGIPFLTTDLTYRCFVSFPLNTG-DLDCETCTITRSGLTGLVIGGLYPVFLAIPVNGGLAARYQSAL
.PMA.IPFL.....YR.FV..PLN.G..L..ET.TI...GL.GLV.GGL...FL.IP.NGGL.ARY.S.L
RetrocopySPMAEIPFLIVHVFYRSFVNLPLN*G<SLEFETHTIK*GGLVGLVFGGL---FLTIPMNGGLEARYESTL
ParentalLPHKGNILSYWIRTSKPVFRKML
L..KGNILSYWIR.SKP.FRKML
RetrocopyLSEKGNILSYWIRISKPDFRKML

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 .00 RPM 13 .57 RPM
SRP007412_cerebellum 0 .00 RPM 4 .80 RPM
SRP007412_heart 0 .00 RPM 23 .72 RPM
SRP007412_kidney 0 .00 RPM 17 .31 RPM
SRP007412_liver 0 .00 RPM 7 .66 RPM
SRP007412_testis 0 .00 RPM 12 .96 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_2165 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2165 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2165 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3306
Gorilla gorilla retro_ggor_1308
Pongo abelii retro_pabe_2726
Macaca mulatta retro_mmul_2073
Parental genes homology:
Parental genes homology involve 28 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000087032 retrocopies
retro_amel_358, retro_amel_422,
Bos taurus ENSBTAG000000004512 retrocopies
retro_btau_1849, retro_btau_223,
Canis familiaris ENSCAFG000000309131 retrocopy
retro_cfam_725,
Callithrix jacchus ENSCJAG000000144661 retrocopy
retro_cjac_4040,
Dasypus novemcinctus ENSDNOG000000043917 retrocopies
retro_dnov_1741, retro_dnov_2634, retro_dnov_2676, retro_dnov_484, retro_dnov_549, retro_dnov_951, retro_dnov_984,
Dipodomys ordii ENSDORG000000064082 retrocopies
retro_dord_120, retro_dord_656,
Erinaceus europaeus ENSEEUG000000091053 retrocopies
retro_eeur_24, retro_eeur_340, retro_eeur_615,
Echinops telfairi ENSETEG000000071802 retrocopies
retro_etel_1693, retro_etel_667,
Felis catus ENSFCAG000000276063 retrocopies
retro_fcat_1015, retro_fcat_1320, retro_fcat_48,
Homo sapiens ENSG000001712022 retrocopies
retro_hsap_1510, retro_hsap_3306,
Gorilla gorilla ENSGGOG000000277422 retrocopies
retro_ggor_1157, retro_ggor_1308,
Macropus eugenii ENSMEUG000000116251 retrocopy
retro_meug_1914,
Microcebus murinus ENSMICG000000055103 retrocopies
retro_mmur_1382, retro_mmur_941, retro_mmur_956,
Myotis lucifugus ENSMLUG000000058963 retrocopies
retro_mluc_1150, retro_mluc_1290, retro_mluc_1951,
Macaca mulatta ENSMMUG000000165422 retrocopies
retro_mmul_2073, retro_mmul_2146,
Mustela putorius furoENSMPUG000000099682 retrocopies
retro_mputfur_1077, retro_mputfur_720,
Mus musculus ENSMUSG000000306153 retrocopies
retro_mmus_1431, retro_mmus_1531, retro_mmus_3555,
Nomascus leucogenys ENSNLEG000000164082 retrocopies
retro_nleu_1751, retro_nleu_2500,
Oryctolagus cuniculus ENSOCUG000000165341 retrocopy
retro_ocun_1120,
Otolemur garnettii ENSOGAG0000000540312 retrocopies
retro_ogar_1020, retro_ogar_2016, retro_ogar_2083, retro_ogar_2118, retro_ogar_2379, retro_ogar_26, retro_ogar_2825, retro_ogar_2883, retro_ogar_3054, retro_ogar_3385, retro_ogar_661, retro_ogar_787,
Pongo abelii ENSPPYG000000037392 retrocopies
retro_pabe_1258, retro_pabe_2726,
Pan troglodytes ENSPTRG00000004134 2 retrocopies
retro_ptro_1022, retro_ptro_2165 ,
Pteropus vampyrus ENSPVAG000000061972 retrocopies
retro_pvam_1411, retro_pvam_254,
Rattus norvegicus ENSRNOG000000227483 retrocopies
retro_rnor_1706, retro_rnor_2844, retro_rnor_918,
Ictidomys tridecemlineatus ENSSTOG000000161012 retrocopies
retro_itri_108, retro_itri_165,
Tupaia belangeri ENSTBEG000000091575 retrocopies
retro_tbel_3441, retro_tbel_3720, retro_tbel_3785, retro_tbel_4072, retro_tbel_4111,
Tarsius syrichta ENSTSYG000000090716 retrocopies
retro_tsyr_1371, retro_tsyr_1457, retro_tsyr_1934, retro_tsyr_580, retro_tsyr_735, retro_tsyr_974,
Tursiops truncatus ENSTTRG000000120082 retrocopies
retro_ttru_1091, retro_ttru_415,


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