RetrogeneDB ID:

retro_hsap_43

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:104697712..104698714(+)
Located in intron of:ENSG00000198431
Retrocopy
information
Ensembl ID:ENSG00000255150
Aliases:EID3, NS4EB, NSE4B, NSMCE4B
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:NSMCE4A
Ensembl ID:ENSG00000107672
Aliases:NSMCE4A, C10orf86, NS4EA, NSE4A
Description:non-SMC element 4 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:25935]


Retrocopy-Parental alignment summary:






>retro_hsap_43
ATGAAGATGGATGTGTCAGTGAGGGCCGCGGGCTGCTCCGACGACCTCAGCTCTGGGGAGGCCGACGTAGACCCAAAGCT
CCTGGAGCTCACCGCTGACGAGGAGAAGTGCCGCAGCATCCGCAGGCAGTACCGGCAGCTCATGTACTGCGTGCGGCAGA
ACCGGGAGGACATCGTGAGCTCGGCGAACAACTCCTTAACCGAGGCTCTGGAGGAAGCCAACGTCCTCTTTGATGGCGTG
AGCCGAACCAGAGAAGCAGCCCTCGACGCCCGGTTTCTTGTTATGGCTTCTGATTTGGGTAAAGAAAAGGCAAAGCAGTT
AAACTCAGATATGAACTTCTTTAATCAGTTAGCATTTTGTGACTTTCTGTTTCTGTTCGTGGGTCTGAATTGGATGGAAG
GCGATCCTGACAAGTTGAGTGATTGTGATGATAGCATAGCTCTTTCCTTCTGGAAGGCAATAGAAAAGGAAGCAACATCC
TGGATGGTAAAAGCTGAGACATTCCATTTTGTTTTTGGTTCATTCAAGCTAGAACGTTCTGCACCAAAGCCCCGACTTGA
ACACCAGAAAAAAGTTCGCAAGATGGAAGAAAATGGCAACATGCCTACAAAGTTGCAGAAGTTGGACCTGAGTAGTTATC
CAGAAGCGACAGAAAAAAACGTAGAAAGGATTTTGGGATTGTTGCAAACCTACTTTCGAAAGTATCCTGATACTCCTGTG
TCCTATTTTGAGTTTGTGATTGATCCAAACTCTTTTTCTCGTACTGTGGAGAATATATTTTATGTTTCTTTTATTGTAAG
AGATGGTTTTGCAAGAATAAGGCTTGATGAAGACAGGCTGCCAATATTAGAGCCGATGAATGTTAACCAAATGGGTGAGG
GAAATGATTCCAGTTGCCATGGCAGGAAACAGGGAGTTATATCTTTGACTTTACAGGAGTGGAAAAACATTGTGGCAGCT
TTTGAAATTTCTGAGGCTATGATTACATACTCCTCATACTAA

ORF - retro_hsap_43 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.68 %
Parental protein coverage: 81.82 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSGDEMMDPASLEAEADQGLCRQIRHQYRALINSVQQNREDILN-AGDKLTEVLEEANTLFNEVSRAREAV
SG....DP..LE..AD...CR.IR.QYR.L...V.QNREDI...A...LTE.LEEAN.LF..VSR.REA.
RetrocopySGEADVDPKLLELTADEEKCRSIRRQYRQLMYCVRQNREDIVSSANNSLTEALEEANVLFDGVSRTREAA
ParentalLDAHFLVLASDLGKEKAKQLRSDLSSFDMLRYVETLLTHMGVNPLEAEELIRDEDSPDFEFIVYDSWKIT
LDA.FLV.ASDLGKEKAKQL.SD...F..L.....L....G.N..E......D..S.....I....WK..
RetrocopyLDARFLVMASDLGKEKAKQLNSDMNFFNQLAFCDFLFLFVGLNWMEGDP---DKLSDCDDSIALSFWKAI
ParentalGRTAENTFNKTHTFHFLLGSIYGECPVPKPRVDRPRKVPVIQEERAMPAQLRRME-ESHQEATEKEVERI
...A.....K..TFHF..GS...E...PKPR.....KV....E...MP..L......S..EATEK.VERI
RetrocopyEKEATSWMVKAETFHFVFGSFKLERSAPKPRLEHQKKVRKMEENGNMPTKLQKLDLSSYPEATEKNVERI
ParentalLGLLQTYFREDPDTPMSFFDFVVDPHSFPRTVENIFHVSFIIRDGFARIRLDQDRLPVIEPVSINEENEG
LGLLQTYFR..PDTP.S.F.FV.DP.SF.RTVENIF.VSFI.RDGFARIRLD.DRLP..EP...N...EG
RetrocopyLGLLQTYFRKYPDTPVSYFEFVIDPNSFSRTVENIFYVSFIVRDGFARIRLDEDRLPILEPMNVNQMGEG
ParentalFEHNTQVRNQGIIALSYRDWEEIVKTFEISEPVITPS
.......R.QG.I.L....W..IV..FEISE..IT.S
RetrocopyNDSSCHGRKQGVISLTLQEWKNIVAAFEISEAMITYS

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 1 .15 RPM 17 .89 RPM
bodymap2_adrenal 3 .48 RPM 38 .97 RPM
bodymap2_brain 2 .86 RPM 10 .92 RPM
bodymap2_breast 2 .22 RPM 42 .53 RPM
bodymap2_colon 1 .12 RPM 22 .00 RPM
bodymap2_heart 0 .52 RPM 12 .94 RPM
bodymap2_kidney 0 .87 RPM 20 .37 RPM
bodymap2_liver 0 .09 RPM 16 .81 RPM
bodymap2_lung 1 .86 RPM 17 .58 RPM
bodymap2_lymph_node 3 .36 RPM 31 .65 RPM
bodymap2_ovary 4 .65 RPM 31 .50 RPM
bodymap2_prostate 1 .44 RPM 44 .56 RPM
bodymap2_skeletal_muscle 0 .15 RPM 15 .64 RPM
bodymap2_testis 47 .64 RPM 13 .20 RPM
bodymap2_thyroid 1 .53 RPM 27 .44 RPM
bodymap2_white_blood_cells 3 .09 RPM 15 .87 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_43 in 10 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 12:104697241..104698017
ENCFF002CFX POLR2A 12:104697242..104698046
ENCFF002CHO POLR2A 12:104697250..104698016
ENCFF002CIH POLR2A 12:104697353..104697857
ENCFF002CIO POLR2A 12:104697476..104697739
ENCFF002CLM POLR2A 12:104697409..104697949
ENCFF002CPG POLR2A 12:104697346..104697836
ENCFF002CQC POLR2A 12:104697329..104697809
ENCFF002CQO POLR2A 12:104697481..104697705
ENCFF002CVJ POLR2A 12:104697279..104697889

EST - click to see more details

3 EST(s) were mapped to retro_hsap_43 retrocopy
EST ID Start End Identity Match Mis-match Score
AF012366 104698118 104698385 98.9 263 2 259
AI955095 104698420 104698559 95.7 133 6 127
AI435861 104698444 104698559 100 115 0 115

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_203711804 libraries22 libraries3 libraries0 libraries0 libraries
TSS #2 TSS_203721778 libraries46 libraries4 libraries0 libraries1 library
TSS #3 TSS_20373705 libraries392 libraries614 libraries72 libraries46 libraries

The graphical summary, for retro_hsap_43 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_43 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_43 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_716
Bos taurus retro_btau_1387
Canis familiaris retro_cfam_379
Equus caballus retro_ecab_109
Parental genes homology:
Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000108971 retrocopy
retro_amel_419,
Bos taurus ENSBTAG000000191661 retrocopy
retro_btau_1387,
Canis familiaris ENSCAFG000000124192 retrocopies
retro_cfam_1427, retro_cfam_379,
Choloepus hoffmanni ENSCHOG000000036951 retrocopy
retro_chof_577,
Dipodomys ordii ENSDORG000000038801 retrocopy
retro_dord_677,
Equus caballus ENSECAG000000166512 retrocopies
retro_ecab_109, retro_ecab_465,
Erinaceus europaeus ENSEEUG000000149061 retrocopy
retro_eeur_124,
Felis catus ENSFCAG000000036471 retrocopy
retro_fcat_994,
Homo sapiens ENSG00000107672 1 retrocopy
retro_hsap_43 ,
Loxodonta africana ENSLAFG000000042141 retrocopy
retro_lafr_1051,
Macaca mulatta ENSMMUG000000120441 retrocopy
retro_mmul_716,
Mustela putorius furoENSMPUG000000029601 retrocopy
retro_mputfur_396,
Nomascus leucogenys ENSNLEG000000169191 retrocopy
retro_nleu_2073,
Otolemur garnettii ENSOGAG000000100261 retrocopy
retro_ogar_280,
Pongo abelii ENSPPYG000000027121 retrocopy
retro_pabe_878,
Pteropus vampyrus ENSPVAG000000171862 retrocopies
retro_pvam_1163, retro_pvam_795,
Rattus norvegicus ENSRNOG000000204521 retrocopy
retro_rnor_2515,
Ictidomys tridecemlineatus ENSSTOG000000111121 retrocopy
retro_itri_36,
Vicugna pacos ENSVPAG000000065341 retrocopy
retro_vpac_260,

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 = 2.74 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .13 RPM
CEU_NA11843 0 .71 RPM
CEU_NA11930 0 .62 RPM
CEU_NA12004 2 .13 RPM
CEU_NA12400 1 .93 RPM
CEU_NA12751 2 .28 RPM
CEU_NA12760 1 .35 RPM
CEU_NA12827 0 .19 RPM
CEU_NA12872 1 .06 RPM
CEU_NA12873 0 .73 RPM
FIN_HG00183 1 .67 RPM
FIN_HG00277 1 .74 RPM
FIN_HG00315 2 .51 RPM
FIN_HG00321 1 .42 RPM
FIN_HG00328 1 .33 RPM
FIN_HG00338 1 .13 RPM
FIN_HG00349 2 .05 RPM
FIN_HG00375 1 .86 RPM
FIN_HG00377 1 .97 RPM
FIN_HG00378 2 .74 RPM
GBR_HG00099 1 .05 RPM
GBR_HG00111 1 .76 RPM
GBR_HG00114 1 .50 RPM
GBR_HG00119 1 .70 RPM
GBR_HG00131 1 .81 RPM
GBR_HG00133 1 .69 RPM
GBR_HG00134 1 .57 RPM
GBR_HG00137 1 .59 RPM
GBR_HG00142 0 .94 RPM
GBR_HG00143 2 .23 RPM
TSI_NA20512 1 .61 RPM
TSI_NA20513 1 .02 RPM
TSI_NA20518 1 .92 RPM
TSI_NA20532 1 .56 RPM
TSI_NA20538 1 .57 RPM
TSI_NA20756 1 .40 RPM
TSI_NA20765 2 .55 RPM
TSI_NA20771 2 .13 RPM
TSI_NA20786 1 .78 RPM
TSI_NA20798 1 .72 RPM
YRI_NA18870 1 .02 RPM
YRI_NA18907 0 .97 RPM
YRI_NA18916 1 .52 RPM
YRI_NA19093 1 .54 RPM
YRI_NA19099 1 .38 RPM
YRI_NA19114 1 .99 RPM
YRI_NA19118 2 .20 RPM
YRI_NA19213 0 .93 RPM
YRI_NA19214 1 .08 RPM
YRI_NA19223 1 .77 RPM

Indel association:

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



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