RetrogeneDB ID:

retro_hsap_574

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:52024866..52026572(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000225137
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DYNC1I2
Ensembl ID:ENSG00000077380
Aliases:DYNC1I2, DNCI2, IC2
Description:dynein, cytoplasmic 1, intermediate chain 2 [Source:HGNC Symbol;Acc:2964]


Retrocopy-Parental alignment summary:






>retro_hsap_574
GTTGCTCCTGTGCAAGAAGAATCAGATCTTGAAAAAAGAAGAAGAGAAGCTGAAGCATTGCTCCAAAGCATGGGGCTAAC
TCCAGAATCCCCCATTGTCCCTCCTCCTATGTCTCCATCCTCCAAATCTGTGAGCACTCCAAGTGAAGCTGGAAGCCAAG
ACTCTGGAGATGGCGCCGTGGGATCTAGACGAGGACCTATTAAACTTGGAATGGCTAAAATCACGCAAGTCGACTTTCCT
CCTCGAGAAATTGTCACGTATACAAAGGAAACTCAGACTCCAGTTATGGCTCAACCCAAAAAAGATGAAGAGGAAGATGA
TGATGTAGTGGCTCCTAAACTACCTATTGAACCTGAAGAAGAGAAAACTTTAAAGAAAGATGAGGAAAATGATAGTAAAG
CTCCCCCCATGAGCTGACTGAAGAAGAAAAGCAACAAATCTTGCACTCTGAGGAATTTTTAAGTTTCTTTGACCATTCTA
CAAGAATTGTAGAAAGAGCTCTTTCTGAGCAGATTAACATCTTCTTTCACTATAGTGGGAGAGATTTGGAAGACAAAGAA
GGAGAGATTCAAGCAGGTGCTAAACTGTCATTAAATTGACAATTTTTTGACGAACGTTGGTCAAAGCATCGGGTTGTTAG
TTGTTTGGATTGGTCATCTCAGTATCCGGAGTTACTCGTGGCTTCCTATAACAACAATGAAGATGCCCCTCATGAGCCTG
ATGGTGTGGCCCTTGTATGGAATATGAAATACAAAAAAACTACCCCAGAGTATGTGTTTCACTGCCAGTCAGCTGTGATG
TCTGCCACATTTGCAAAATTTCATCCAAATCTTGTTGTTGGTGGTACATATTCAGGCCAAACTGTGCTTTGGGATAACCG
TAGCAATAAAAGAACTCCAGTGCAAAGAACTCCACTGTCAGCAGCTGCACACACACACCCTGTATATTGTGTAAACGTTG
TTGGAACACAAAATGCTCACAATCTGATTAGCATCTCTACTGATGGAAAAATTTGTTCATGGAGTCTGGACATGCTTTCC
CATCCACAGGATAGCATGGAGTTGGTTCATAAACAGTCAAAAGCAGTAGCTGTGACATCTATGTCCTTCCCTGTTGGAGA
TGTCAACAACTTTGTTGTTGGGAGTGAAGAAGGTTCTGTGTACACAGCATGCCACCATGGCAGCAAAGCTGGAATCAGTG
AGATGTTTGAGGGGCATCAAGGACCAATCACTGGCATCCATTGTCATGCAGCTGTTGGAGCAGTAGACTTCTCACATCTT
TATGTCACTTCATCATTTGACTGGACAGTAAAGCTTTGGACAACTAAGAATAACAAGCCTTTGTATTCATTTGAAGACAA
TGCAGACTATGTTTATGATGTTATGTGGTCACCTACCCACCCAGCCCTGTTTGCCTGTGTGGATGGCATGGGGAGATTGG
ATTTGTGGAATCTCAATAATGACACAGAGGTACCAACTGCCAGCATTTCTGTGGAGGGTAATCCTGCTCTTAATCATGTG
AGATGGACCCATTCTGGCAGAGAGATTGCTGTGGGTGATTCTGAAGGACAGATTGCTATATACGATGTGGGAGAGCAGAT
TGCTGTTCCCCGCAATGATGAATGGGCATGGTTTGGCTGAACACTTGCAGAAATTAATGCAAACCGAGCTGATGCAGAGG
AGGAAGCAGCTACCCGAATACCTGCT

ORF - retro_hsap_574 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.72 %
Parental protein coverage: 92.97 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVAPVQEESDLEKKRREAEALLQSMGLTPESPIVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLG
VAPVQEESDLEK.RREAEALLQSMGLTPESPIVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLG
RetrocopyVAPVQEESDLEKRRREAEALLQSMGLTPESPIVPPPMSPSSKSVSTPSEAGSQDSGDGAVGSRRGPIKLG
ParentalMAKITQVDFPPREIVTYTKETQTPVMAQPKEDEEEDDDVVAPKPPIEPEEEKTLKKDEENDSKAPP-HEL
MAKITQVDFPPREIVTYTKETQTPVMAQPK.DEEEDDDVVAPK.PIEPEEEKTLKKDEENDSKAPP.HEL
RetrocopyMAKITQVDFPPREIVTYTKETQTPVMAQPKKDEEEDDDVVAPKLPIEPEEEKTLKKDEENDSKAPP<HEL
ParentalTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFDYSGRDLEDKEGEIQAGAKLSLNRQFFDERWSK
TEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFF.YSGRDLEDKEGEIQAGAKLSLN.QFFDERWSK
RetrocopyTEEEKQQILHSEEFLSFFDHSTRIVERALSEQINIFFHYSGRDLEDKEGEIQAGAKLSLN*QFFDERWSK
ParentalHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLV
HRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLV
RetrocopyHRVVSCLDWSSQYPELLVASYNNNEDAPHEPDGVALVWNMKYKKTTPEYVFHCQSAVMSATFAKFHPNLV
ParentalVGGTYSGQIVLWDNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHP
VGGTYSGQ.VLWDNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHP
RetrocopyVGGTYSGQTVLWDNRSNKRTPVQRTPLSAAAHTHPVYCVNVVGTQNAHNLISISTDGKICSWSLDMLSHP
ParentalQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACRHGSKAGISEMFEGHQGPITGIHCHAAV
QDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTAC.HGSKAGISEMFEGHQGPITGIHCHAAV
RetrocopyQDSMELVHKQSKAVAVTSMSFPVGDVNNFVVGSEEGSVYTACHHGSKAGISEMFEGHQGPITGIHCHAAV
ParentalGAVDFSHLFVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDT
GAVDFSHL.VTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDT
RetrocopyGAVDFSHLYVTSSFDWTVKLWTTKNNKPLYSFEDNADYVYDVMWSPTHPALFACVDGMGRLDLWNLNNDT
ParentalEVPTASISVEGNPALNRVRWTHSGREIAVGDSEGQIVIYDVGEQIAVPRNDEWARFGRTLAEINANRADA
EVPTASISVEGNPALN.VRWTHSGREIAVGDSEGQI.IYDVGEQIAVPRNDEWA.FG.TLAEINANRADA
RetrocopyEVPTASISVEGNPALNHVRWTHSGREIAVGDSEGQIAIYDVGEQIAVPRNDEWAWFG*TLAEINANRADA
ParentalEEEAATRIPA
EEEAATRIPA
RetrocopyEEEAATRIPA

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 .42 RPM 71 .34 RPM
bodymap2_adrenal 0 .25 RPM 60 .24 RPM
bodymap2_brain 1 .13 RPM 160 .17 RPM
bodymap2_breast 0 .31 RPM 67 .10 RPM
bodymap2_colon 0 .68 RPM 123 .07 RPM
bodymap2_heart 0 .13 RPM 56 .99 RPM
bodymap2_kidney 0 .35 RPM 100 .90 RPM
bodymap2_liver 0 .00 RPM 15 .59 RPM
bodymap2_lung 0 .09 RPM 72 .26 RPM
bodymap2_lymph_node 0 .09 RPM 63 .12 RPM
bodymap2_ovary 0 .60 RPM 97 .54 RPM
bodymap2_prostate 0 .12 RPM 124 .20 RPM
bodymap2_skeletal_muscle 0 .13 RPM 40 .94 RPM
bodymap2_testis 0 .60 RPM 111 .29 RPM
bodymap2_thyroid 0 .85 RPM 83 .89 RPM
bodymap2_white_blood_cells 0 .04 RPM 68 .28 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_574 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_574 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_5177469 libraries716 libraries612 libraries23 libraries9 libraries

The graphical summary, for retro_hsap_574 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_574 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_574 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000071961 retrocopy
retro_cjac_3204,
Homo sapiens ENSG00000077380 1 retrocopy
retro_hsap_574 ,
Tursiops truncatus ENSTTRG000000113551 retrocopy
retro_ttru_237,

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 = 0.5 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .13 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .36 RPM
CEU_NA12004 0 .19 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .17 RPM
CEU_NA12760 0 .18 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .19 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .41 RPM
FIN_HG00277 0 .18 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .15 RPM
FIN_HG00328 0 .17 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .23 RPM
FIN_HG00375 0 .20 RPM
FIN_HG00377 0 .18 RPM
FIN_HG00378 0 .17 RPM
GBR_HG00099 0 .26 RPM
GBR_HG00111 0 .11 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .17 RPM
GBR_HG00131 0 .14 RPM
GBR_HG00133 0 .07 RPM
GBR_HG00134 0 .07 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .17 RPM
GBR_HG00143 0 .22 RPM
TSI_NA20512 0 .23 RPM
TSI_NA20513 0 .19 RPM
TSI_NA20518 0 .50 RPM
TSI_NA20532 0 .14 RPM
TSI_NA20538 0 .23 RPM
TSI_NA20756 0 .35 RPM
TSI_NA20765 0 .15 RPM
TSI_NA20771 0 .43 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .41 RPM
YRI_NA18907 0 .14 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .16 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .12 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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