RetrogeneDB ID:

retro_hsap_3306

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:38763913..38764389(-)
Located in intron of:ENSG00000249740
Retrocopy
information
Ensembl ID:ENSG00000248577
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM126A
Ensembl ID:ENSG00000171202
Aliases:TMEM126A, OPA7
Description:transmembrane protein 126A [Source:HGNC Symbol;Acc:25382]


Retrocopy-Parental alignment summary:






>retro_hsap_3306
ATGGAAAATCAGGAGCCAGATAGCACTTTCAAGGAAAACGTAATTTTAGGCATCATAACTAGAAAAATTAACCAGCTTCC
AGAAGCAGAAAGGAAACTACTTGAACATGGATCAATATATGTTGAACTTAATGCTGTTCTCCGTGGCCTAATAGCAAACA
GTCTTTTTCTATGCATCTTGAACATGACACAGGCTCATATAGCTGTCGGCTCACCAATGGCAGAGAACCCATTTCTGATA
GTACATGTATTTTACAGAAGTTTTGTAAATTTACCTTTGAATTGAGGTCATTGGAATTTGAAACCCATACCATAAAATGA
GGTGGATTGGTTGGTCTTGTTTTTGGTGGTCTTTTCTTGACTATACCTATGAATGGTGGCTTAGAAGCCAGATATGAATC
AACTCTGTTATCAGAGAAAGGAAACATCTTAAGTTACTGGATTAGAATTTCTAAGCCTGACTTTAGAAAGATGTTG

ORF - retro_hsap_3306 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.8 %
Parental protein coverage: 82.05 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMENHKSNN--KENITIVDISRKINQLPEAERNLLENGSVYVGLNAALCGLIANSLFRRILNVTKARIAAG
MEN.......KEN.....I.RKINQLPEAER.LLE.GS.YV.LNA.L.GLIANSLF..ILN.T.A.IA.G
RetrocopyMENQEPDSTFKENVILGIITRKINQLPEAERKLLEHGSIYVELNAVLRGLIANSLFLCILNMTQAHIAVG
ParentalLPMAGIPFLTTDLTYRCFVSFPLNTG-DLDCETCTITRSGLTGLVIGGLYPVFLAIPVNGGLAARYQSAL
.PMA..PFL.....YR.FV..PLN.G..L..ET.TI...GL.GLV.GGL...FL.IP.NGGL.ARY.S.L
RetrocopySPMAENPFLIVHVFYRSFVNLPLN*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
bodymap2_adipose 0 .00 RPM 8 .59 RPM
bodymap2_adrenal 0 .00 RPM 10 .36 RPM
bodymap2_brain 0 .00 RPM 14 .02 RPM
bodymap2_breast 0 .00 RPM 21 .11 RPM
bodymap2_colon 0 .00 RPM 15 .49 RPM
bodymap2_heart 0 .00 RPM 26 .23 RPM
bodymap2_kidney 0 .00 RPM 17 .52 RPM
bodymap2_liver 0 .00 RPM 18 .91 RPM
bodymap2_lung 0 .00 RPM 10 .36 RPM
bodymap2_lymph_node 0 .00 RPM 11 .66 RPM
bodymap2_ovary 0 .00 RPM 14 .80 RPM
bodymap2_prostate 0 .00 RPM 16 .13 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .78 RPM
bodymap2_testis 0 .00 RPM 23 .13 RPM
bodymap2_thyroid 0 .00 RPM 16 .91 RPM
bodymap2_white_blood_cells 0 .00 RPM 11 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3306 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3306 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3306 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3306 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3306 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2165
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 ENSG00000171202 2 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 ENSPTRG000000041342 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,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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