RetrogeneDB ID:

retro_hsap_430

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:103565698..103566263(-)
Located in intron of:ENSG00000060718
Retrocopy
information
Ensembl ID:ENSG00000234257
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SOD2
Ensembl ID:ENSG00000112096
Aliases:SOD2, IPOB, MNSOD, MVCD6
Description:superoxide dismutase 2, mitochondrial [Source:HGNC Symbol;Acc:11180]


Retrocopy-Parental alignment summary:






>retro_hsap_430
TACAGCCTCCTAGGCTTATCTTATTATTATGGTGCCCTGGGGCCTAATATTAATGTACACATCATGCAGCTAAACCACAG
AAAATACCAGGTCATTGGGTGAATAACTTGACTGCCTTCAAGGAGAAATAAAAAGAGGTTCTGGTAAAAGGTGATGTTAG
AATCCAGATAGCTCTTCAGCCTGCACTTAAGTTCAGTGGTAGAGACCATATTACTCTTACCATTTTATGGACAAACCTCA
GCCTCAGTGGTAGTGGAGGATTGAAAGGGGAGTTTCTGGGAGCCATCAAATATTAGTTTTGTTCCTTTGATTAACTTAAG
GAGAAGCTGACAGATGTATCTGTTAGTATTCAAAGTTCCAGTTGTGGTTGGCTTGGTTTCATTAAGTAAAAGAACTCTTA
TAGATCATTGCTTGTCCTAATCAGGATCCATTATAAAGGTCATCAGGACTTATTCTACTTTTGGGGATTGGTGTATGGAA
GTTCTCTTAACTGTCTTCAGCATAAAAAATGTCAGAGTTGATTATCCAAAAGCTTTTTTGGAGTGTAATCAACTGAGAGA
ATGTA

ORF - retro_hsap_430 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.03 %
Parental protein coverage: 84.68 %
Number of stop codons detected: 7
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalHSLPDLPYDYGALEPHINAQIMQLHHSKHHAA-YVNNLNVTEEKYQEALAKGDVTAQIALQPALKFNGGG
.SL..L.Y.YGAL.P.IN..IMQL.H.K......VNNL....EK..E.L.KGDV..QIALQPALKF.G..
RetrocopyYSLLGLSYYYGALGPNINVHIMQLNHRKYQVI<WVNNLTAFKEK*KEVLVKGDVRIQIALQPALKFSGRD
ParentalHINHSIFWTNLSPNGGGEPKGELLEAIKRDFGSFDKFKEKLTAASVGVQGSGWGWLGFNKERGH-LQIAA
HI...I.WTNLS..G.G..KGE.L.AIK..F.SFD..KEKLT..SV..Q.S..GWLGF.K.....L.I.A
RetrocopyHITLTILWTNLSLSGSGGLKGEFLGAIKY*FCSFD*LKEKLTDVSVSIQSSSCGWLGFIK*KNS<L*IIA
ParentalCPNQDPLQGTTGLIPLLGIDVWEHA-YYLQYK-NVRPDYLKA-IWNVINWENV
CPNQDPL....GLI.LLGI.VW......LQ.K.NVR.DY.KA..W.VIN.ENV
RetrocopyCPNQDPL*RSSGLILLLGIGVWKFS>NCLQHK>NVRVDYPKA>FWSVIN*ENV

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 2446 .84 RPM
bodymap2_adrenal 0 .00 RPM 796 .83 RPM
bodymap2_brain 0 .00 RPM 550 .21 RPM
bodymap2_breast 0 .00 RPM 645 .01 RPM
bodymap2_colon 0 .00 RPM 1356 .51 RPM
bodymap2_heart 0 .00 RPM 893 .85 RPM
bodymap2_kidney 0 .00 RPM 3928 .09 RPM
bodymap2_liver 0 .00 RPM 655 .40 RPM
bodymap2_lung 0 .00 RPM 2107 .44 RPM
bodymap2_lymph_node 0 .00 RPM 1234 .90 RPM
bodymap2_ovary 0 .00 RPM 439 .11 RPM
bodymap2_prostate 0 .00 RPM 1136 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 21906 .20 RPM
bodymap2_testis 0 .00 RPM 479 .47 RPM
bodymap2_thyroid 0 .00 RPM 2842 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 1266 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_430 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_430 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_430 retrocopy 5' end.

Lab - click to see more details

retro_hsap_430 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_430 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_327
Gorilla gorilla retro_ggor_419
Parental genes homology:
Parental genes homology involve 24 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000154661 retrocopy
retro_amel_786,
Canis familiaris ENSCAFG000000006711 retrocopy
retro_cfam_1795,
Choloepus hoffmanni ENSCHOG000000032154 retrocopies
retro_chof_1952, retro_chof_1966, retro_chof_2620, retro_chof_937,
Callithrix jacchus ENSCJAG000000116641 retrocopy
retro_cjac_3032,
Dasypus novemcinctus ENSDNOG000000079071 retrocopy
retro_dnov_1653,
Equus caballus ENSECAG000000117972 retrocopies
retro_ecab_70, retro_ecab_840,
Echinops telfairi ENSETEG000000164001 retrocopy
retro_etel_731,
Felis catus ENSFCAG000000028431 retrocopy
retro_fcat_1200,
Homo sapiens ENSG00000112096 1 retrocopy
retro_hsap_430 ,
Gorilla gorilla ENSGGOG000000082121 retrocopy
retro_ggor_419,
Myotis lucifugus ENSMLUG000000122421 retrocopy
retro_mluc_528,
Monodelphis domestica ENSMODG000000075211 retrocopy
retro_mdom_373,
Mustela putorius furoENSMPUG000000050451 retrocopy
retro_mputfur_1382,
Nomascus leucogenys ENSNLEG000000110611 retrocopy
retro_nleu_1023,
Otolemur garnettii ENSOGAG000000171001 retrocopy
retro_ogar_1123,
Pongo abelii ENSPPYG000000171431 retrocopy
retro_pabe_292,
Pan troglodytes ENSPTRG000000187571 retrocopy
retro_ptro_327,
Pteropus vampyrus ENSPVAG000000053021 retrocopy
retro_pvam_288,
Rattus norvegicus ENSRNOG000000190481 retrocopy
retro_rnor_2221,
Sarcophilus harrisii ENSSHAG000000147951 retrocopy
retro_shar_210,
Ictidomys tridecemlineatus ENSSTOG000000087381 retrocopy
retro_itri_1432,
Tupaia belangeri ENSTBEG000000021001 retrocopy
retro_tbel_665,
Tarsius syrichta ENSTSYG000000004571 retrocopy
retro_tsyr_183,
Tursiops truncatus ENSTTRG000000143641 retrocopy
retro_ttru_265,

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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