RetrogeneDB ID:

retro_hsap_3538

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:154870638..154871373(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220181
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C6orf203
Ensembl ID:ENSG00000130349
Aliases:C6orf203, PRED31
Description:chromosome 6 open reading frame 203 [Source:HGNC Symbol;Acc:17971]


Retrocopy-Parental alignment summary:






>retro_hsap_3538
GTTATAAGTGCCATGGCTATGACTAGTGTCAAATTGCATGCTGGTGTTTTAAGAAAGCCAGATACCTGGATTGGACTCTC
GGGTGTTCTCTGAGGAACACCTTCATCACACAAACTCTGTACTTCCTGGAATCAGTACTTGTATTTTTCTAGTACCAAGT
TACATGCACCAAATTATAATACACTTTTCTATAACATTTTCTCACTGAGACTCCCGGGGCTTTTAATATCTCTGGAATAT
TTTTTTCCATTTTCCATAAGACTCAAAAGTAATATAAGCTCTACAAAATCTACTAAAAAGTATCTGCAAAAAATAGGAGA
TGAGGAGGACTCTGATGCAGAAAGTGATCAGAACGAGATGAGTGAGCAGGAAGAGGAGCTTGAGGATGGCCTTACTATAG
CAAAGACTATCAAGACCTGGAAACAGTAGTGCGGTCTTTTCAGGATGACGTTGTCCTGAAGACAAGCCTGGATATTGGAA
GAAACAAAGTGGAAGATGCATTCTGCAAAGGTGAATTCAGGCTGAATGGGGAAAAATTATGGAAGAAAAGCAGAATGGTC
AAAGTGGGAGATACATTGGATCTTCTCATTGGAGAGGATAAGGAAGCAGGAACAGAGACAGTGATGCAGATTCTCCCAAA
AAAAAGTGTTTGAAGAGAAGGCTGAAAGTGAAAAATACACAGTGGTATTACAGCAGTGGAAAAACTTAAAAATGCCTAAG
AAGAGAATGTCTAAA

ORF - retro_hsap_3538 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.35 %
Parental protein coverage: 99.59 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalIISAMAMASVKLLAGVLRKPDAWIGLWGVLRGTPSSYKLCTSWNRYLYFSSTKLRAPNYKTLFYNIFSLR
.ISAMAM.SVKL.AGVLRKPD.WIGL.GVL.GTPSS.KLCTSWN.YLYFSSTKL.APNY.TLFYNIFSLR
RetrocopyVISAMAMTSVKLHAGVLRKPDTWIGLSGVL*GTPSSHKLCTSWNQYLYFSSTKLHAPNYNTLFYNIFSLR
ParentalLPGLLLSPECIFPFSVRLKSNIRSTKSTKKSLQKV-DEEDSDEESHHDEMSEQEEELEDDPTVV-KNYKD
LPGLL.S.E..FPFS.RLKSNI.STKSTKK.LQK..DEEDSD.ES...EMSEQEEELED..T...K.Y.D
RetrocopyLPGLLISLEYFFPFSIRLKSNISSTKSTKKYLQKIGDEEDSDAESDQNEMSEQEEELEDGLTIA<KDYQD
ParentalLEKAVQSFRYDVVLKTGLDIGRNKVEDAFYKGELRLNEEKLWKKSRTVKVGDTLDLLIGEDKEAGTETVM
LE..V.SF..DVVLKT.LDIGRNKVEDAF.KGE.RLN.EKLWKKSR.VKVGDTLDLLIGEDKEAGTETVM
RetrocopyLETVVRSFQDDVVLKTSLDIGRNKVEDAFCKGEFRLNGEKLWKKSRMVKVGDTLDLLIGEDKEAGTETVM
ParentalRIL-LKKVFEEKTESEKYRVVLRRWKSLKLPKKRMSK
.IL....VFEEK.ESEKY.VVL..WK.LK.PKKRMSK
RetrocopyQIL>XXXVFEEKAESEKYTVVLQQWKNLKMPKKRMSK

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 7 .43 RPM
bodymap2_adrenal 0 .00 RPM 13 .94 RPM
bodymap2_brain 0 .00 RPM 11 .63 RPM
bodymap2_breast 0 .00 RPM 15 .41 RPM
bodymap2_colon 0 .00 RPM 13 .77 RPM
bodymap2_heart 0 .00 RPM 14 .77 RPM
bodymap2_kidney 0 .00 RPM 24 .88 RPM
bodymap2_liver 0 .00 RPM 10 .60 RPM
bodymap2_lung 0 .00 RPM 2 .50 RPM
bodymap2_lymph_node 0 .00 RPM 10 .95 RPM
bodymap2_ovary 0 .00 RPM 17 .75 RPM
bodymap2_prostate 0 .00 RPM 12 .44 RPM
bodymap2_skeletal_muscle 0 .00 RPM 8 .80 RPM
bodymap2_testis 0 .00 RPM 17 .63 RPM
bodymap2_thyroid 0 .00 RPM 17 .87 RPM
bodymap2_white_blood_cells 0 .00 RPM 8 .11 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_3538 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3538 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3538 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3538 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3538 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2405
Gorilla gorilla retro_ggor_2389
Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000037321 retrocopy
retro_cfam_1818,
Homo sapiens ENSG00000130349 1 retrocopy
retro_hsap_3538 ,
Gorilla gorilla ENSGGOG000000061131 retrocopy
retro_ggor_2389,
Macropus eugenii ENSMEUG000000135341 retrocopy
retro_meug_2181,
Microcebus murinus ENSMICG000000041371 retrocopy
retro_mmur_1269,
Macaca mulatta ENSMMUG000000073911 retrocopy
retro_mmul_115,
Nomascus leucogenys ENSNLEG000000134502 retrocopies
retro_nleu_1433, retro_nleu_499,
Otolemur garnettii ENSOGAG000000088392 retrocopies
retro_ogar_1396, retro_ogar_390,
Pongo abelii ENSPPYG000000168851 retrocopy
retro_pabe_2922,
Pan troglodytes ENSPTRG000000184642 retrocopies
retro_ptro_1453, retro_ptro_2405,
Tursiops truncatus ENSTTRG000000088372 retrocopies
retro_ttru_324, retro_ttru_432,

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 = 0.05 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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 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 .02 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 .03 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 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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