RetrogeneDB ID:

retro_hsap_1733

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:20687957..20689037(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226549
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SCD
Ensembl ID:ENSG00000099194
Aliases:SCD, FADS5, MSTP008, SCD1, SCDOS
Description:stearoyl-CoA desaturase (delta-9-desaturase) [Source:HGNC Symbol;Acc:10571]


Retrocopy-Parental alignment summary:






>retro_hsap_1733
ATGCCGGCCCACTTGCTGCAGGACGATATCTCTAGCTCCTATACCACCACCACCACCACCATTACAGCGCCTCCTTCCAG
GGTCCCGCAGAATGGAGGAGATAAGTTGGAGACGACGCCCCTCTACTTGGAAGAAGACATTCGCCCTGATATAAAAGATG
ATATATATAACCTCACCTACAAGGATAAGGAAGGCCCAAGCCCCAAGGTTGAATATGTCTGGAGAAACATCATCCTTATG
TCTCTGCTACACTTGGGCGCCCTGTATGGGATCACTTTGATTCCTACCTGCAACTTATACACCTGGCTTTGGGGGGTATT
CTACTATTTTATCAGTGCCCTGGGCATAACAGCAGGAGCTCATCCTCTGTGGAGCCACTGATCTTACAAAGCTCGGCTGT
CCCTGTGGCTCTTTCTGATCATTGCCAACACAATGGCATTCCAGAATGATGTCTATGAATGGGCTCGCGACCACCGTGCC
CACCACAAGTTTTCAGAAACACATGCTGATCCTCATAATTCCTGACGTGGCTTTTTCTTCTCTCACGTGGGTTGGCTGCT
TGTGCGCAAACACCCAACTGTCAAAGAGAAGGGCAGTACGCTAGACTTGTCTGACCTAGAAGCCGAGAAACTGGTGATGT
TCCAGAGGAGGTACTACAAACCCGGCTTGCTGTTGATGTGCTTCATCCTGCCCACGCTTGTGCCCTGGTGTTTCTGGGGT
GAAACTTTTCAAAACAGCGTGTTCGTTGCCACTTTCTTGCGATATGCTGTGGTGCTTAATGCCACGTGGCTGGTGAACAG
TGCTGCCCACCTCTTCAGATATCGTCCTTATGACAAGAACATTAGCCTCCGGGAGAATATCCTGGTTTCACTTGGAGCTG
TGGGTGAGGGCTTTCACAACTACCACCACTCCTTTCCCTATGACTACTCTGCCAGTGAGTACCGCTGGCACATCAACTTC
ACCACATTCTTCATTGATTGCATGGCCGCCTTCGGTCTGGCCTACGACCAGAAGAAAGTCTCCAAGGCCGCCATCTTGGC
CAGGATTAAAAGAACCGGAGAGGGAAACTACAAGAGTGGC

ORF - retro_hsap_1733 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.22 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPAHLLQDDISSSYTTTTTI-TAPPSRVLQNGGDKLETMPLYLEDDIRPDIKDDIYDPTYKDKEGPSPKV
MPAHLLQDDISSSY.......TAPPSRV.QNGGDKLET.PLYLE.DIRPDIKDDIY..TYKDKEGPSPKV
RetrocopyMPAHLLQDDISSSYXXXXXXXTAPPSRVPQNGGDKLETTPLYLEEDIRPDIKDDIYNLTYKDKEGPSPKV
ParentalEYVWRNIILMSLLHLGALYGITLIPTCKFYTWLWGVFYYFVSALGITAGAHRLWSHRSYKARLPLRLFLI
EYVWRNIILMSLLHLGALYGITLIPTC..YTWLWGVFYYF.SALGITAGAH.LWSH.SYKARL.L.LFLI
RetrocopyEYVWRNIILMSLLHLGALYGITLIPTCNLYTWLWGVFYYFISALGITAGAHPLWSH*SYKARLSLWLFLI
ParentalIANTMAFQNDVYEWARDHRAHHKFSETHADPHNSRRGFFFSHVGWLLVRKHPAVKEKGSTLDLSDLEAEK
IANTMAFQNDVYEWARDHRAHHKFSETHADPHNS.RGFFFSHVGWLLVRKHP.VKEKGSTLDLSDLEAEK
RetrocopyIANTMAFQNDVYEWARDHRAHHKFSETHADPHNS*RGFFFSHVGWLLVRKHPTVKEKGSTLDLSDLEAEK
ParentalLVMFQRRYYKPGLLMMCFILPTLVPWYFWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLFGYRPYDKN
LVMFQRRYYKPGLL.MCFILPTLVPW.FWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLF.YRPYDKN
RetrocopyLVMFQRRYYKPGLLLMCFILPTLVPWCFWGETFQNSVFVATFLRYAVVLNATWLVNSAAHLFRYRPYDKN
ParentalISPRENILVSLGAVGEGFHNYHHSFPYDYSASEYRWHINFTTFFIDCMAALGLAYDRKKVSKAAILARIK
IS.RENILVSLGAVGEGFHNYHHSFPYDYSASEYRWHINFTTFFIDCMAA.GLAYD.KKVSKAAILARIK
RetrocopyISLRENILVSLGAVGEGFHNYHHSFPYDYSASEYRWHINFTTFFIDCMAAFGLAYDQKKVSKAAILARIK
ParentalRTGDGNYKSG
RTG.GNYKSG
RetrocopyRTGEGNYKSG

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 .02 RPM 232 .41 RPM
bodymap2_adrenal 0 .00 RPM 64 .70 RPM
bodymap2_brain 0 .09 RPM 1497 .40 RPM
bodymap2_breast 1 .11 RPM 6662 .60 RPM
bodymap2_colon 0 .00 RPM 59 .03 RPM
bodymap2_heart 0 .00 RPM 10 .49 RPM
bodymap2_kidney 0 .00 RPM 15 .18 RPM
bodymap2_liver 0 .00 RPM 432 .27 RPM
bodymap2_lung 0 .00 RPM 144 .43 RPM
bodymap2_lymph_node 0 .04 RPM 55 .19 RPM
bodymap2_ovary 0 .02 RPM 352 .94 RPM
bodymap2_prostate 0 .00 RPM 34 .17 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .46 RPM
bodymap2_testis 0 .00 RPM 89 .40 RPM
bodymap2_thyroid 0 .00 RPM 126 .64 RPM
bodymap2_white_blood_cells 0 .00 RPM 4 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1733 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1733 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_562531474 libraries260 libraries66 libraries3 libraries26 libraries
TSS #2 TSS_56254432 libraries454 libraries704 libraries157 libraries82 libraries

The graphical summary, for retro_hsap_1733 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1733 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1733 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3058
Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000173382 retrocopies
retro_cjac_1077, retro_cjac_2348,
Homo sapiens ENSG00000099194 1 retrocopy
retro_hsap_1733 ,
Macaca mulatta ENSMMUG000000108171 retrocopy
retro_mmul_1636,
Pongo abelii ENSPPYG000000025661 retrocopy
retro_pabe_1545,
Pan troglodytes ENSPTRG000000028471 retrocopy
retro_ptro_3058,
Drosophila melanogaster FBgn00866871 retrocopy
retro_dmel_78,

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 = 0.14 RPM Legend:


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