RetrogeneDB ID:

retro_hsap_2507

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:21:37502786..37503671(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226054
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MEMO1
Ensembl ID:ENSG00000162959
Aliases:MEMO1, C2orf4, MEMO, NS5ATP7
Description:mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]


Retrocopy-Parental alignment summary:






>retro_hsap_2507
ATGTCCAACCGAGTGGTCTGCCGAGAAGCCAGTCACGCCGGGAGCTGGTACACAGCCTCAGGACCGCAGCTGAATGCACA
GCTAGAAGGTTGGCTTTCACAAGTACAGTCTACAAAAAGACCTGCTAGAGCCATTATTGCCCCCCATGCAGGATATACGT
ACTGTGGGTCTTGTGCTGCCCATGCTTATAAACAAGTGGATCCGTCTATTACCCGGAGAATTTTCATCCTTGGGCCTTCT
CATCATGTGCCCCTCTCTCGATGTGCACTTTCCAGTGTGGATATATATAGGACACCCCTGTATGACCTTCGTATTGACCA
AAAGATTTACGGAGAACTATGGAAGACAGGAATGTTTGAACGCATGTCTCTGCAGACAGATGAAGATGAACGCAGTATTG
AAATGCATTTGCCTTATACAGCTAAAGCCATGGAAAGCCATAAGGATGAGTTTACCATTATTCCTTTACTGGTTGGAGCT
CTGAGTCAAAAGAACAGGAATTCGGAACTTTTCAGTAAATATCTAGCGGATCCTAGTAATCTCTTTGTGGTTTCTTCTGA
TTTCTGCCATTGGGGTCAAAGGTTCCGTCACAGTTACTATGATGAATCCCAGGGGGAGATTTGTAGATCCATTGAACATC
TAGATAAAATGGGTATGAGTATTATAGAACAATTAGACCCTGTATCTTTTAGCAATTACTTGAAGAAATACCATAATACT
ATATGTGGAAGACATCCCATTGGGGTGTTATTAAATGCTATCACAGAGCTCCAGAAGAATGGAATGAATATGAGTTTTTC
GTTTTTGAATTATGCCCAGTCGAGCCAGTGTAGAAACTGGCAAGACAGTTCAGTGAGTTATGCAGCTGGAGCACTCACGG
TCCAC

ORF - retro_hsap_2507 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.62 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSNRVVCREASHAGSWYTASGPQLNAQLEGWLSQVQSTKRPARAIIAPHAGYTYCGSCAAHAYKQVDPSI
MSNRVVCREASHAGSWYTASGPQLNAQLEGWLSQVQSTKRPARAIIAPHAGYTYCGSCAAHAYKQVDPSI
RetrocopyMSNRVVCREASHAGSWYTASGPQLNAQLEGWLSQVQSTKRPARAIIAPHAGYTYCGSCAAHAYKQVDPSI
ParentalTRRIFILGPSHHVPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDEHSIEMHLPYT
TRRIFILGPSHHVPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDE.SIEMHLPYT
RetrocopyTRRIFILGPSHHVPLSRCALSSVDIYRTPLYDLRIDQKIYGELWKTGMFERMSLQTDEDERSIEMHLPYT
ParentalAKAMESHKDEFTIIPVLVGALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYYDESQGEIY
AKAMESHKDEFTIIP.LVGALS.........LFSKYLADPSNLFVVSSDFCHWGQRFR.SYYDESQGEI.
RetrocopyAKAMESHKDEFTIIPLLVGALSQKNRN--SELFSKYLADPSNLFVVSSDFCHWGQRFRHSYYDESQGEIC
ParentalRSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNGMNMSFSFLNYAQSSQCR
RSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNGMNMSFSFLNYAQSSQCR
RetrocopyRSIEHLDKMGMSIIEQLDPVSFSNYLKKYHNTICGRHPIGVLLNAITELQKNGMNMSFSFLNYAQSSQCR
ParentalNWQDSSVSYAAGALTVH
NWQDSSVSYAAGALTVH
RetrocopyNWQDSSVSYAAGALTVH

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 .48 RPM 0 .44 RPM
bodymap2_adrenal 0 .63 RPM 0 .88 RPM
bodymap2_brain 0 .77 RPM 0 .75 RPM
bodymap2_breast 0 .66 RPM 0 .47 RPM
bodymap2_colon 0 .64 RPM 0 .23 RPM
bodymap2_heart 0 .55 RPM 0 .39 RPM
bodymap2_kidney 0 .50 RPM 0 .12 RPM
bodymap2_liver 0 .40 RPM 0 .40 RPM
bodymap2_lung 0 .33 RPM 0 .44 RPM
bodymap2_lymph_node 1 .63 RPM 0 .27 RPM
bodymap2_ovary 0 .52 RPM 0 .19 RPM
bodymap2_prostate 1 .02 RPM 0 .28 RPM
bodymap2_skeletal_muscle 1 .51 RPM 0 .49 RPM
bodymap2_testis 1 .11 RPM 1 .45 RPM
bodymap2_thyroid 0 .55 RPM 0 .38 RPM
bodymap2_white_blood_cells 2 .60 RPM 0 .20 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2507 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 21:37502379..37502809
ENCFF002CFX POLR2A 21:37502392..37502788

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2507 retrocopy
EST ID Start End Identity Match Mis-match Score
BE162119 37502827 37502987 100 160 0 160

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_1049411314 libraries322 libraries184 libraries6 libraries3 libraries
TSS #2 TSS_1049421545 libraries270 libraries14 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_2507 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_2507 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2507 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000077711 retrocopy
retro_amel_1500,
Equus caballus ENSECAG000000199461 retrocopy
retro_ecab_401,
Echinops telfairi ENSETEG000000079941 retrocopy
retro_etel_561,
Felis catus ENSFCAG000000013851 retrocopy
retro_fcat_642,
Homo sapiens ENSG00000162959 2 retrocopies
retro_hsap_2507 , retro_hsap_3522,
Myotis lucifugus ENSMLUG000000161081 retrocopy
retro_mluc_1923,
Mus musculus ENSMUSG000000587041 retrocopy
retro_mmus_834,
Nomascus leucogenys ENSNLEG000000155771 retrocopy
retro_nleu_488,
Oryctolagus cuniculus ENSOCUG000000058783 retrocopies
retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii ENSOGAG000000109753 retrocopies
retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii ENSPPYG000000125111 retrocopy
retro_pabe_2910,

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 = 1.55 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .58 RPM
CEU_NA11843 0 .31 RPM
CEU_NA11930 0 .88 RPM
CEU_NA12004 0 .65 RPM
CEU_NA12400 0 .14 RPM
CEU_NA12751 0 .41 RPM
CEU_NA12760 0 .67 RPM
CEU_NA12827 0 .61 RPM
CEU_NA12872 0 .46 RPM
CEU_NA12873 0 .41 RPM
FIN_HG00183 0 .38 RPM
FIN_HG00277 0 .70 RPM
FIN_HG00315 0 .44 RPM
FIN_HG00321 0 .51 RPM
FIN_HG00328 0 .24 RPM
FIN_HG00338 0 .49 RPM
FIN_HG00349 0 .74 RPM
FIN_HG00375 0 .73 RPM
FIN_HG00377 0 .55 RPM
FIN_HG00378 0 .28 RPM
GBR_HG00099 0 .38 RPM
GBR_HG00111 0 .39 RPM
GBR_HG00114 0 .50 RPM
GBR_HG00119 0 .41 RPM
GBR_HG00131 0 .43 RPM
GBR_HG00133 0 .43 RPM
GBR_HG00134 0 .41 RPM
GBR_HG00137 0 .38 RPM
GBR_HG00142 0 .67 RPM
GBR_HG00143 0 .51 RPM
TSI_NA20512 0 .42 RPM
TSI_NA20513 0 .77 RPM
TSI_NA20518 1 .55 RPM
TSI_NA20532 0 .34 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .52 RPM
TSI_NA20765 0 .31 RPM
TSI_NA20771 0 .71 RPM
TSI_NA20786 0 .50 RPM
TSI_NA20798 0 .75 RPM
YRI_NA18870 0 .64 RPM
YRI_NA18907 0 .66 RPM
YRI_NA18916 0 .34 RPM
YRI_NA19093 0 .55 RPM
YRI_NA19099 0 .56 RPM
YRI_NA19114 0 .45 RPM
YRI_NA19118 0 .52 RPM
YRI_NA19213 0 .53 RPM
YRI_NA19214 0 .47 RPM
YRI_NA19223 0 .52 RPM

Indel association:

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





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