RetrogeneDB ID:

retro_hsap_854

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:17457221..17457728(-)
Located in intron of:ENSG00000006071
Retrocopy
information
Ensembl ID:ENSG00000255035
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SDHC
Ensembl ID:ENSG00000143252
Aliases:None
Description:succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa [Source:HGNC Symbol;Acc:10682]


Retrocopy-Parental alignment summary:






>retro_hsap_854
ATGGCTGTGCTCTTGCTGAGACATGTTGGTTGTCATTGCCTCCGAGCCCACTTTAGCCCTCAGCTCTGTACCAGAAATGC
TGTTCCTTTGGGAATCACAGCCAAAGAAGAGATGGAGCAGTTCTGGAATAAGAACACAAGTTCAAACTGTCCCATATCTC
CCCACATCACTATCTACAGTTGGTCTCTTCCCATGGCGATGTCCATCTGCCACCGTGGCACTGGTATTGCTTTGAGTGCA
GGGGTCTCTCTTTTTGGCATGTTGGCCCTGTTACTCCCTGGGAACTTTGAGTCTTATTTGGAATGCGTGAAGTCCCTGTG
TCCGGGGCCAGCACTGATCCACACAGCTAAGTTTGCACTCATCTTCCCTCTCATGTATCATATCTGGAATGGGGTCTGAC
ACTTGATGTGGGACCTAGGAAAAGGCCTGAAGATTCCCCAGCTATACCAATCTGGAGTGGTTGTCCCGGTTCTTACTGTA
CTGTCCTCTGTAGGGCTGGCAGCCATG

ORF - retro_hsap_854 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.35 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAALLLRHVGRHCLRAHFSPQLCIRNAVPLGTTAKEEMERFWNKNIGSNRPLSPHITIYSWSLPMAMSIC
MA.LLLRHVG.HCLRAHFSPQLC.RNAVPLG.TAKEEME.FWNKN..SN.P.SPHITIYSWSLPMAMSIC
RetrocopyMAVLLLRHVGCHCLRAHFSPQLCTRNAVPLGITAKEEMEQFWNKNTSSNCPISPHITIYSWSLPMAMSIC
ParentalHRGTGIALSAGVSLFGMSALLLPGNFESYLELVKSLCLGPALIHTAKFALVFPLMYHTWNGIRHLMWDLG
HRGTGIALSAGVSLFGM.ALLLPGNFESYLE.VKSLC.GPALIHTAKFAL.FPLMYH.WNG..HLMWDLG
RetrocopyHRGTGIALSAGVSLFGMLALLLPGNFESYLECVKSLCPGPALIHTAKFALIFPLMYHIWNGV*HLMWDLG
ParentalKGLKIPQLYQSGVVVLVLTVLSSMGLAAM
KGLKIPQLYQSGVVV.VLTVLSS.GLAAM
RetrocopyKGLKIPQLYQSGVVVPVLTVLSSVGLAAM

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 29 .62 RPM
bodymap2_adrenal 0 .00 RPM 28 .39 RPM
bodymap2_brain 0 .05 RPM 27 .35 RPM
bodymap2_breast 0 .00 RPM 49 .86 RPM
bodymap2_colon 0 .00 RPM 28 .17 RPM
bodymap2_heart 0 .02 RPM 59 .78 RPM
bodymap2_kidney 0 .02 RPM 67 .92 RPM
bodymap2_liver 0 .00 RPM 53 .21 RPM
bodymap2_lung 0 .00 RPM 36 .64 RPM
bodymap2_lymph_node 0 .00 RPM 33 .50 RPM
bodymap2_ovary 0 .00 RPM 28 .72 RPM
bodymap2_prostate 0 .00 RPM 40 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 32 .85 RPM
bodymap2_testis 0 .04 RPM 26 .92 RPM
bodymap2_thyroid 0 .04 RPM 43 .61 RPM
bodymap2_white_blood_cells 0 .00 RPM 47 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_854 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_854 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_854 retrocopy 5' end.

Lab - click to see more details

retro_hsap_854 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_854 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_697
Macaca mulatta retro_mmul_1063
Parental genes homology:
Parental genes homology involve 17 parental genes, and 41 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000153512 retrocopies
retro_amel_468, retro_amel_803,
Bos taurus ENSBTAG000000158531 retrocopy
retro_btau_835,
Canis familiaris ENSCAFG000000129922 retrocopies
retro_cfam_1529, retro_cfam_275,
Callithrix jacchus ENSCJAG000000047573 retrocopies
retro_cjac_1119, retro_cjac_2455, retro_cjac_988,
Echinops telfairi ENSETEG000000157671 retrocopy
retro_etel_675,
Felis catus ENSFCAG000000004991 retrocopy
retro_fcat_1609,
Homo sapiens ENSG00000143252 4 retrocopies
retro_hsap_1794, retro_hsap_1896, retro_hsap_609, retro_hsap_854 ,
Gorilla gorilla ENSGGOG000000080173 retrocopies
retro_ggor_1390, retro_ggor_536, retro_ggor_697,
Macaca mulatta ENSMMUG0000001241111 retrocopies
retro_mmul_1063, retro_mmul_1323, retro_mmul_1338, retro_mmul_1686, retro_mmul_1845, retro_mmul_2002, retro_mmul_2087, retro_mmul_239, retro_mmul_2416, retro_mmul_369, retro_mmul_672,
Mustela putorius furoENSMPUG000000144391 retrocopy
retro_mputfur_1201,
Nomascus leucogenys ENSNLEG000000143673 retrocopies
retro_nleu_1476, retro_nleu_420, retro_nleu_439,
Pteropus vampyrus ENSPVAG000000055442 retrocopies
retro_pvam_879, retro_pvam_974,
Rattus norvegicus ENSRNOG000000031632 retrocopies
retro_rnor_1486, retro_rnor_1487,
Sarcophilus harrisii ENSSHAG000000168351 retrocopy
retro_shar_205,
Sus scrofa ENSSSCG000000303182 retrocopies
retro_sscr_1050, retro_sscr_1061,
Takifugu rubripes ENSTRUG000000018731 retrocopy
retro_trub_41,
Tursiops truncatus ENSTTRG000000092341 retrocopy
retro_ttru_196,

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 ) > 0 RPM = 0.02 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 .02 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).





Copyright © RetrogeneDB 2014-2017