RetrogeneDB ID:

retro_hsap_2554

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:30938559..30940067(+)
Located in intron of:ENSG00000214491
Retrocopy
information
Ensembl ID:ENSG00000225774
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SIRPA
Ensembl ID:ENSG00000198053
Aliases:SIRPA, BIT, CD172A, MFR, MYD-1, P84, PTPNS1, SHPS1, SIRP
Description:signal-regulatory protein alpha [Source:HGNC Symbol;Acc:9662]


Retrocopy-Parental alignment summary:






>retro_hsap_2554
ATGGAGCCCGCGGGCCGGTCCCCGGCCGCCTCGGGCCGCTGCTCTGCCTGCTGCTCCCCGCGTCCTGCGCCTGGTCAGGA
GTGGCGGGTGAGGAGGAGCTGCAGGTGATTCAGCCTGAGAAGTCTGTATCAGTTGCAGCTGGAGAGTCGGCCGCTCTGCA
GTGCACTGTGACCTCCCTGAACCCTGTGGGGCCCATCCAACGGTTCAGAGGAGCTGGACCAGGCCGGAAATTAATCTACC
ATCAAAAAGAAGGCCACTTCCCCCGGGTAACAACTGTTTCAGATCTCACAAAGAGAACCAACATGGACTTTTCCATCTGC
ATCAGTAACATCACCCCAGCAGATGCCGGCACCTACTACTGTGTGAAGTTCCAGAAAGGGAGCCCTGACGTGGAGTTGAA
GTCTGGAGCAGGCACTGAGCTGTCTGTGCGTGCCAAACCCTCTGCCCCCGTGGTATCGGGCCCCGCAGCGAGGGCCACAC
CTGACCACACAGTGAGCTTCACCTGCGAGTCTCATGGCTTCTCACCCAGAGACATCAGCCTGAAATGGTTCAAAAATGGG
AATCAGCTCTCAGACTTCCAGACCAACGTGGACCCCGCAAGAGAGAGCGTGTCCTACAGCATCCACAGCACAGCCAATGT
GGTGCTGACCCGCGGGGACATTCACTCTCAAGTCATCTGCGAGGTGGCCCACGTCACCTTGCGGGGGGACTCTTTTCGTG
GGACTGCCAACTTGTCTGAGACTATCCAAGTTCCACCCACCTTGGAGGTTACTCAACAGCCCATGAGGGCAGAGAACCAG
GTGAATATCACCTGCCAGGTGACGAAATTCTACCCCCAGAGACTACAGTTGACCTGGTTGGAGAACGGCAATGTGTCCCG
GACAGAAACGGCCTCAACTCTTACAGAGAACAAGGATGGCACCTACAACTGGATGAGCTGGCTCCTGGTGAATGTATCTG
CCCACAGGGATGATGTGAAGCTCACCTGCCAGGTGGAGCATGACGGGCAGTCAGCGGTCAGCAAAAGCCATGACCTGAAG
GTCTCAGCCCACCTGAAGGAGCAGAGCTCAAATACCGCCGCTGAGAACACTGGACCTAATGAACAGAACATCTATATTGT
GGTGGGCGTGGTGTGCACCTTGCTGGTGGCCCTACTGATGGAGGCTCTCTACCTCGTCCGAATCAGACAGAAGAAAGCCC
AGGGCTCCACTTCTTCTACAAGGTTGCATGAACCCGAGAAGAATGCCAGAAAAATAACCCAGGACACAAATGATATCACA
TATGCGGACCTGAACCTGCCCAAGGGGAAGAAGCCTGCTCCCCGGGCCGCGGAGCCCAACAACCACACAGAGTATGCCAG
CATTCAGACCAGCCTGCAGCCTGCGTCGGAGGACACCCTCACCTATGCTGACCTGGACATGGTGCACCTCAACCGGACCC
CCAAGCAGCTGGCCCCCAAGCCCGAGCTGTCCTTCTCAGAGTATGCCAGCATCCAGGTCCCGAGGAAG

ORF - retro_hsap_2554 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.69 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEPAG-PAPGRLGPLLCLLLAASCAWSGVAGEEELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWF
MEPAG.P.PGRLGPLLCLLL.ASCAWSGVAGEEELQVIQP.KSV.VAAGE.A.L.CT.TSL.PVGPIQ.F
RetrocopyMEPAG<PVPGRLGPLLCLLLPASCAWSGVAGEEELQVIQPEKSVSVAAGESAALQCTVTSLNPVGPIQRF
ParentalRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPDDVEFKSGAG
RGAGPGR.LIY.QKEGHFPRVTTVSDLTKR.NMDFSI.I.NITPADAGTYYCVKF.KGSPD.VE.KSGAG
RetrocopyRGAGPGRKLIYHQKEGHFPRVTTVSDLTKRTNMDFSICISNITPADAGTYYCVKFQKGSPD-VELKSGAG
ParentalTELSVRAKPSAPVVSGPAARATPQHTVSFTCESHGFSPRDITLKWFKNGNELSDFQTNVDPVGESVSYSI
TELSVRAKPSAPVVSGPAARATP.HTVSFTCESHGFSPRDI.LKWFKNGN.LSDFQTNVDP..ESVSYSI
RetrocopyTELSVRAKPSAPVVSGPAARATPDHTVSFTCESHGFSPRDISLKWFKNGNQLSDFQTNVDPARESVSYSI
ParentalHSTAKVVLTREDVHSQVICEVAHVTLQGDPLRGTANLSETIRVPPTLEVTQQPVRAENQVNVTCQVRKFY
HSTA.VVLTR.D.HSQVICEVAHVTL.GD..RGTANLSETI.VPPTLEVTQQP.RAENQVN.TCQV.KFY
RetrocopyHSTANVVLTRGDIHSQVICEVAHVTLRGDSFRGTANLSETIQVPPTLEVTQQPMRAENQVNITCQVTKFY
ParentalPQRLQLTWLENGNVSRTETASTVTENKDGTYNWMSWLLVNVSAHRDDVKLTCQVEHDGQPAVSKSHDLKV
PQRLQLTWLENGNVSRTETAST.TENKDGTYNWMSWLLVNVSAHRDDVKLTCQVEHDGQ.AVSKSHDLKV
RetrocopyPQRLQLTWLENGNVSRTETASTLTENKDGTYNWMSWLLVNVSAHRDDVKLTCQVEHDGQSAVSKSHDLKV
ParentalSAHPKEQGSNTAAENTGSNERNIYIVVGVVCTLLVALLMAALYLVRIRQKKAQGSTSSTRLHEPEKNARE
SAH.KEQ.SNTAAENTG.NE.NIYIVVGVVCTLLVALLM.ALYLVRIRQKKAQGSTSSTRLHEPEKNAR.
RetrocopySAHLKEQSSNTAAENTGPNEQNIYIVVGVVCTLLVALLMEALYLVRIRQKKAQGSTSSTRLHEPEKNARK
ParentalITQDTNDITYADLNLPKGKKPAPQAAEPNNHTEYASIQTSPQPASEDTLTYADLDMVHLNRTPKQPAPKP
ITQDTNDITYADLNLPKGKKPAP.AAEPNNHTEYASIQTS.QPASEDTLTYADLDMVHLNRTPKQ.APKP
RetrocopyITQDTNDITYADLNLPKGKKPAPRAAEPNNHTEYASIQTSLQPASEDTLTYADLDMVHLNRTPKQLAPKP
ParentalEPSFSEYASVQVPRK
E.SFSEYAS.QVPRK
RetrocopyELSFSEYASIQVPRK

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 .16 RPM 170 .95 RPM
bodymap2_adrenal 0 .00 RPM 68 .98 RPM
bodymap2_brain 0 .09 RPM 204 .49 RPM
bodymap2_breast 0 .04 RPM 65 .29 RPM
bodymap2_colon 0 .00 RPM 48 .75 RPM
bodymap2_heart 0 .00 RPM 22 .41 RPM
bodymap2_kidney 0 .21 RPM 46 .57 RPM
bodymap2_liver 0 .09 RPM 59 .57 RPM
bodymap2_lung 0 .11 RPM 74 .79 RPM
bodymap2_lymph_node 0 .07 RPM 84 .84 RPM
bodymap2_ovary 0 .06 RPM 58 .68 RPM
bodymap2_prostate 0 .26 RPM 50 .54 RPM
bodymap2_skeletal_muscle 0 .00 RPM 35 .87 RPM
bodymap2_testis 0 .26 RPM 36 .12 RPM
bodymap2_thyroid 0 .04 RPM 20 .77 RPM
bodymap2_white_blood_cells 0 .79 RPM 230 .74 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2554 in 3 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CKX POLR2A 22:30938415..30938835
ENCFF002CMI POLR2A 22:30938433..30938803
ENCFF002DBE POLR2A 22:30938385..30938881

EST - click to see more details

No EST(s) were mapped for retro_hsap_2554 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_107720734 libraries481 libraries407 libraries102 libraries105 libraries

The graphical summary, for retro_hsap_2554 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_2554 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2554 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000198053 1 retrocopy
retro_hsap_2554 ,
Sorex araneus ENSSARG000000138881 retrocopy
retro_sara_435,

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 = 0.19 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .10 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 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .13 RPM
YRI_NA19093 0 .13 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .10 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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