RetrogeneDB ID:

retro_hsap_1944

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:57677220..57678306(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000256704
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SDCCAG3
Ensembl ID:ENSG00000165689
Aliases:SDCCAG3, NY-CO-3
Description:serologically defined colon cancer antigen 3 [Source:HGNC Symbol;Acc:10667]


Retrocopy-Parental alignment summary:






>retro_hsap_1944
GATTTGGGCTATGGAAAGGGGAAATGTTCTAAGCAGAGCCCGTCAGGAGCCCACGAGACACATTTTGGAGATGACAAATT
TGAAGATCTTGAAGAGGCAAATCCATTCTCCTTTAAAGAGTTTCTGAAGACCAAGAACATCGGCCTGTCAAAAGAGGACC
CGGTCAGCAGAATTTATGCAAAGGAAGCGTCGAGGCATTCACTGGGACTTGACCACAACTCCCCACTCTCCCAAACCGGG
GGGTATGGCCTGGAGTATCGGCAGCCATTTTTCGAGGACCCGACAGGGGCCGGTGACCTCCTGGATGAGGAGGAGGATGA
GGACACCGGATGGAGTGGGGCCTACCTGCCGTCCGCCATCCAGCAGACTCACCCGGAGAGGGTCCCTGCCTGCACGTCGC
CCTGCAGCACATACCTTTCCTTTTTCTCCACCCCGTCAGAGCTGGCAGGGCCCGAGTCTCTGCTCCCGTGGGCGTTGAGT
GACACTGATTCTCGCGTGTCTCCGGCCTCTCCGGCAGGGAGTCCTAGCACCGATTTTGCGGCTCAGGGAGAGTCTCTGGG
AGACAGGCACCTGCGGACGCTGCAGATAAGTTACGAAGCACTGAAAGGTGAAAATTCTAAGCTGAGAAGAAAGCTGAATG
AGATTCAGAGCTTCTCTGAAGCTCAAACAGAAATGGTGAGGACGCTTGTGCGGAAATTAGAAGCAAAAATGATCAACGAG
GAAAGCGACTACCACGACTTGGAGTTGGTGGTTCAGCAGGTGGAGCAGAACCTGGAGCTGATGACCAAACGGGCTGTAAA
GGCAGAAAACCATGTCGTGAAACTGAAACAGGAAATCAGTTTGCTGCAGGCGCAGGTCTCCAGCTTCCAGCGAGAGAATG
AAGCCTTGCGGTGCGACCAGGGGGCCAGCCTGACAGTGGTGAAGCAGAACGCCGACGTGGCCTTGCAGAACCTCTGGGTG
GTCATGAACAGCGCACAGGCTTCCATTAAGCAACTGGTTTCCAGAGCTGAGATACTGAATCTTGCTGCCGAAATCCTTAA
ATCTGTAGACAGAATTTCTGAAATTAAAGACGAGGAGGAAGACTCT

ORF - retro_hsap_1944 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.99 %
Parental protein coverage: 83.22 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDFGYGKGKCSKQSPSGAHGTHFGDDRFEDLEEANPFSFREFLKTKNLGLSKEDPASRIYAKEASRHSLGL
D.GYGKGKCSKQSPSGAH.THFGDD.FEDLEEANPFSF.EFLKTKN.GLSKEDP.SRIYAKEASRHSLGL
RetrocopyDLGYGKGKCSKQSPSGAHETHFGDDKFEDLEEANPFSFKEFLKTKNIGLSKEDPVSRIYAKEASRHSLGL
ParentalDHNSPPSQTGGYGLEYQQPFFEDPTGAGDLLDEEEDEDTGWSGAYLPSAIEQTHPERVPAGTSPCSTYLS
DHNSP.SQTGGYGLEY.QPFFEDPTGAGDLLDEEEDEDTGWSGAYLPSAI.QTHPERVPA.TSPCSTYLS
RetrocopyDHNSPLSQTGGYGLEYRQPFFEDPTGAGDLLDEEEDEDTGWSGAYLPSAIQQTHPERVPACTSPCSTYLS
ParentalFFSTPSELAGPESLPSWALSDTDSRVSPASPAGSPSADFAVHGESLGDRHLRTLQISYDALKDENSKLRR
FFSTPSELAGPESL..WALSDTDSRVSPASPAGSPS.DFA..GESLGDRHLRTLQISY.ALK.ENSKLRR
RetrocopyFFSTPSELAGPESLLPWALSDTDSRVSPASPAGSPSTDFAAQGESLGDRHLRTLQISYEALKGENSKLRR
ParentalKLNEVQSFSEAQTEMVRTLERKLEAKMIKEESDYHDLESVVQQVEQNLELMTKRAVKAENHVVKLKQEIS
KLNE.QSFSEAQTEMVRTL.RKLEAKMI.EESDYHDLE.VVQQVEQNLELMTKRAVKAENHVVKLKQEIS
RetrocopyKLNEIQSFSEAQTEMVRTLVRKLEAKMINEESDYHDLELVVQQVEQNLELMTKRAVKAENHVVKLKQEIS
ParentalLLQAQVSNFQRENEALRCGQGASLTVVKQNADVALQNLRVVMNSAQASIKQLVSGAETLNLVAEILKSID
LLQAQVS.FQRENEALRC.QGASLTVVKQNADVALQNL.VVMNSAQASIKQLVS.AE.LNL.AEILKS.D
RetrocopyLLQAQVSSFQRENEALRCDQGASLTVVKQNADVALQNLWVVMNSAQASIKQLVSRAEILNLAAEILKSVD
ParentalRISEVKDEEEDS
RISE.KDEEEDS
RetrocopyRISEIKDEEEDS

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 13 .24 RPM
bodymap2_adrenal 0 .00 RPM 30 .11 RPM
bodymap2_brain 0 .00 RPM 7 .57 RPM
bodymap2_breast 0 .00 RPM 16 .03 RPM
bodymap2_colon 0 .02 RPM 16 .94 RPM
bodymap2_heart 0 .00 RPM 8 .92 RPM
bodymap2_kidney 0 .00 RPM 16 .81 RPM
bodymap2_liver 0 .00 RPM 29 .95 RPM
bodymap2_lung 0 .00 RPM 12 .94 RPM
bodymap2_lymph_node 0 .00 RPM 44 .46 RPM
bodymap2_ovary 0 .00 RPM 18 .83 RPM
bodymap2_prostate 0 .00 RPM 21 .49 RPM
bodymap2_skeletal_muscle 0 .00 RPM 11 .48 RPM
bodymap2_testis 0 .21 RPM 21 .47 RPM
bodymap2_thyroid 0 .00 RPM 15 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 12 .09 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1944 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1944 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1944 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1944 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1944 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1300
Gorilla gorilla retro_ggor_1414
Parental genes homology:
Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000165689 1 retrocopy
retro_hsap_1944 ,
Gorilla gorilla ENSGGOG000000109051 retrocopy
retro_ggor_1414,
Mus musculus ENSMUSG000000269273 retrocopies
retro_mmus_1545, retro_mmus_3492, retro_mmus_711,
Nomascus leucogenys ENSNLEG000000081861 retrocopy
retro_nleu_891,
Otolemur garnettii ENSOGAG000000158721 retrocopy
retro_ogar_3418,
Pongo abelii ENSPPYG000000197722 retrocopies
retro_pabe_1612, retro_pabe_256,
Pan troglodytes ENSPTRG000000215551 retrocopy
retro_ptro_1300,
Rattus norvegicus ENSRNOG000000188762 retrocopies
retro_rnor_1215, retro_rnor_2770,

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 = 0.24 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .10 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .22 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .11 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .12 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .06 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



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