RetrogeneDB ID:

retro_hsap_325

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:236646464..236647766(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000244457
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ENO1
Ensembl ID:ENSG00000074800
Aliases:ENO1, ENO1L1, MPB1, NNE, PPH
Description:enolase 1, (alpha) [Source:HGNC Symbol;Acc:3350]


Retrocopy-Parental alignment summary:






>retro_hsap_325
ATGTCTATTCTCAAGATCCATGCCAGGGAGCTCTTTGACTCTCGTGGGAATCCCACTGTTGAGGTTGATCTCTTCACCTC
AGAAGGTCTCTTCAGAGCTGCTGTGCCCAGTGGTGCTTCAACTGGTATCTATGAGGTCCTAGAGCTCCAGGACAATGATA
AGACTCGCTATATGGGGAAGGGTGTCTCAAAGCCTGTTGAGCCCATCAATAAAACTATTGCACCTGTCCTGGTTAGCAAG
AAACTGAACGTCACAGAACAAGAGAAGATTGACAAACTTATGATAGAGATGGATGGAACAGAAAATAAATCTAAATTTGG
TGCAAATGCCATTCTGGGAGTGTCCCTCGCTGCCTGCAAAGCTAGTGCTGTTGAGAAGGGGGTTCCCCTGTACCACCACA
TCGCCGACTTGTCTGGCAACTCCAAAGTCATCTTGCCAGTCCCGGTGTTCAATGTCATCAATGGCAGTTCTCATGCTGTC
ACCAAGCTGGCCATGCAGGAGTTCATGGTCCTCCCAGTCGGTGCAGCAAACTTCAGGGAAGCCATGCCCATTGGAGCGGA
GGTTTACCACAGCCTGAAGAATGTCATCAAGGAGAAATATGGGAAAGATGCCACCGGTGTGGGGGATGGAGGCGCGTTTG
CTCCCAACATCCTGGAGAATAAAGAAGGCCTGGAGCTGCTGAAGACTGCGATTGGGAAAGCTGGCTACACTGATAAGGTG
ATCGTCAGCATGGACGTAGAGGCCTCCGAGTTCTTCAGGTCTGGAAAGTATGACCTGGAATTCAAGTTTCTCGACGACCC
CACCAGGTACATCTCACCTGACTGTCTGGCTGACCTGTACAAGTCCTTCATCAAAAACTACCCAGTGGTGTCTACTGAAG
ATCCCTTTGACCAGGATGACTGGGGAGCTTGGCAGAAGTTCACGGCCAGTGCAGGAATCCAGGTAGTGGAGGATGATCTC
AGAGTGACCAACCCAAAGAGGACAGCCTCGGCCGTGAATGAGAAGAAGTGCAACTGCCTCCTGCTCAAAGTGAACCAGAT
TCGCTCTGTGACTGAGTCCCTTCAGGCGTGCAAGCTGGCCCAGGCCAATGGTTGGTGTGTCATGGTGCCTCATCATTCTG
GGGAGACTGAAAATACCTTCATCACTGACCTGGTGGTGGGGCTGTGACCTGGGCAGCTCAAGACTGGTGCCCCTTGCTGA
TCTGAGCGCTTGGCCAAGTACAACCAGCTCCTCAGAATTGAAGAGGAGCTGGGCAGCAAGGCTAAGTTTGCCGGCAGGAA
CTTCAGAAACCCCCCAGCCAAG

ORF - retro_hsap_325 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.71 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSILKIHAREIFDSRGNPTVEVDLFTSKGLFRAAVPSGASTGIYEALELRDNDKTRYMGKGVSKAVEHIN
MSILKIHARE.FDSRGNPTVEVDLFTS.GLFRAAVPSGASTGIYE.LEL.DNDKTRYMGKGVSK.VE.IN
RetrocopyMSILKIHARELFDSRGNPTVEVDLFTSEGLFRAAVPSGASTGIYEVLELQDNDKTRYMGKGVSKPVEPIN
ParentalKTIAPALVSKKLNVTEQEKIDKLMIEMDGTENKSKFGANAILGVSLAVCKAGAVEKGVPLYRHIADLAGN
KTIAP.LVSKKLNVTEQEKIDKLMIEMDGTENKSKFGANAILGVSLA.CKA.AVEKGVPLY.HIADL.GN
RetrocopyKTIAPVLVSKKLNVTEQEKIDKLMIEMDGTENKSKFGANAILGVSLAACKASAVEKGVPLYHHIADLSGN
ParentalSEVILPVPAFNVINGGSHAGNKLAMQEFMILPVGAANFREAMRIGAEVYHNLKNVIKEKYGKDATNVGDE
S.VILPVP.FNVING.SHA..KLAMQEFM.LPVGAANFREAM.IGAEVYH.LKNVIKEKYGKDAT.VGD.
RetrocopySKVILPVPVFNVINGSSHAVTKLAMQEFMVLPVGAANFREAMPIGAEVYHSLKNVIKEKYGKDATGVGDG
ParentalGGFAPNILENKEGLELLKTAIGKAGYTDKVVIGMDVAASEFFRSGKYDLDFKSPDDPSRYISPDQLADLY
G.FAPNILENKEGLELLKTAIGKAGYTDKV...MDV.ASEFFRSGKYDL.FK..DDP.RYISPD.LADLY
RetrocopyGAFAPNILENKEGLELLKTAIGKAGYTDKVIVSMDVEASEFFRSGKYDLEFKFLDDPTRYISPDCLADLY
ParentalKSFIKDYPVVSIEDPFDQDDWGAWQKFTASAGIQVVGDDLTVTNPKRIAKAVNEKSCNCLLLKVNQIGSV
KSFIK.YPVVS.EDPFDQDDWGAWQKFTASAGIQVV.DDL.VTNPKR.A.AVNEK.CNCLLLKVNQI.SV
RetrocopyKSFIKNYPVVSTEDPFDQDDWGAWQKFTASAGIQVVEDDLRVTNPKRTASAVNEKKCNCLLLKVNQIRSV
ParentalTESLQACKLAQANGWGVMVSHRSGETEDTFIADLVVGLCTGQIKTGAPCRSERLAKYNQLLRIEEELGSK
TESLQACKLAQANGW.VMV.H.SGETE.TFI.DLVVGL..GQ.KTGAPC.SERLAKYNQLLRIEEELGSK
RetrocopyTESLQACKLAQANGWCVMVPHHSGETENTFITDLVVGL*PGQLKTGAPC*SERLAKYNQLLRIEEELGSK
ParentalAKFAGRNFRNPLAK
AKFAGRNFRNP.AK
RetrocopyAKFAGRNFRNPPAK

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 .12 RPM 562 .37 RPM
bodymap2_adrenal 1 .15 RPM 632 .24 RPM
bodymap2_brain 0 .09 RPM 478 .22 RPM
bodymap2_breast 1 .52 RPM 672 .81 RPM
bodymap2_colon 0 .00 RPM 387 .12 RPM
bodymap2_heart 0 .55 RPM 88 .76 RPM
bodymap2_kidney 2 .28 RPM 982 .22 RPM
bodymap2_liver 0 .06 RPM 431 .32 RPM
bodymap2_lung 0 .95 RPM 411 .50 RPM
bodymap2_lymph_node 1 .88 RPM 382 .19 RPM
bodymap2_ovary 0 .77 RPM 434 .37 RPM
bodymap2_prostate 8 .33 RPM 357 .68 RPM
bodymap2_skeletal_muscle 0 .00 RPM 166 .69 RPM
bodymap2_testis 1 .96 RPM 364 .62 RPM
bodymap2_thyroid 3 .82 RPM 392 .14 RPM
bodymap2_white_blood_cells 1 .95 RPM 556 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_325 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_325 retrocopy
EST ID Start End Identity Match Mis-match Score
EL736024 236646464 236647073 99.9 607 1 606

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_91455442 libraries 740 libraries 613 libraries 26 libraries 8 libraries

The graphical summary, for retro_hsap_325 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_325 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_325 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_261
Parental genes homology:
Parental genes homology involve 13 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000034832 retrocopies
retro_chof_1289, retro_chof_1811,
Callithrix jacchus ENSCJAG000000003594 retrocopies
retro_cjac_1963, retro_cjac_2238, retro_cjac_3891, retro_cjac_438,
Erinaceus europaeus ENSEEUG000000086022 retrocopies
retro_eeur_23, retro_eeur_243,
Homo sapiens ENSG00000074800 1 retrocopy
retro_hsap_325 ,
Macropus eugenii ENSMEUG0000000594211 retrocopies
retro_meug_1445, retro_meug_1521, retro_meug_353, retro_meug_472, retro_meug_494, retro_meug_652, retro_meug_664, retro_meug_765, retro_meug_794, retro_meug_874, retro_meug_888,
Macropus eugenii ENSMEUG000000078401 retrocopy
retro_meug_96,
Monodelphis domestica ENSMODG000000095211 retrocopy
retro_mdom_1794,
Mus musculus ENSMUSG000000635241 retrocopy
retro_mmus_109,
Otolemur garnettii ENSOGAG000000040011 retrocopy
retro_ogar_1059,
Ochotona princeps ENSOPRG000000094921 retrocopy
retro_opri_969,
Pan troglodytes ENSPTRG000000001091 retrocopy
retro_ptro_261,
Rattus norvegicus ENSRNOG000000178951 retrocopy
retro_rnor_112,
Sarcophilus harrisii ENSSHAG000000055221 retrocopy
retro_shar_304,

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 = 7.43 RPM Legend:


Library Retrogene expression
CEU_NA11831 1 .03 RPM
CEU_NA11843 3 .61 RPM
CEU_NA11930 7 .43 RPM
CEU_NA12004 2 .89 RPM
CEU_NA12400 4 .17 RPM
CEU_NA12751 6 .17 RPM
CEU_NA12760 2 .69 RPM
CEU_NA12827 2 .64 RPM
CEU_NA12872 2 .97 RPM
CEU_NA12873 2 .71 RPM
FIN_HG00183 2 .55 RPM
FIN_HG00277 2 .66 RPM
FIN_HG00315 1 .90 RPM
FIN_HG00321 3 .02 RPM
FIN_HG00328 1 .89 RPM
FIN_HG00338 3 .07 RPM
FIN_HG00349 1 .20 RPM
FIN_HG00375 3 .08 RPM
FIN_HG00377 1 .99 RPM
FIN_HG00378 3 .55 RPM
GBR_HG00099 3 .40 RPM
GBR_HG00111 4 .19 RPM
GBR_HG00114 2 .24 RPM
GBR_HG00119 1 .41 RPM
GBR_HG00131 5 .52 RPM
GBR_HG00133 2 .77 RPM
GBR_HG00134 4 .87 RPM
GBR_HG00137 5 .66 RPM
GBR_HG00142 1 .97 RPM
GBR_HG00143 3 .80 RPM
TSI_NA20512 3 .96 RPM
TSI_NA20513 0 .85 RPM
TSI_NA20518 1 .78 RPM
TSI_NA20532 1 .97 RPM
TSI_NA20538 1 .47 RPM
TSI_NA20756 2 .24 RPM
TSI_NA20765 3 .13 RPM
TSI_NA20771 3 .04 RPM
TSI_NA20786 4 .16 RPM
TSI_NA20798 3 .27 RPM
YRI_NA18870 6 .57 RPM
YRI_NA18907 4 .82 RPM
YRI_NA18916 2 .93 RPM
YRI_NA19093 1 .59 RPM
YRI_NA19099 3 .57 RPM
YRI_NA19114 5 .74 RPM
YRI_NA19118 2 .86 RPM
YRI_NA19213 4 .71 RPM
YRI_NA19214 4 .18 RPM
YRI_NA19223 4 .78 RPM

Indel association:

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



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