RetrogeneDB ID:

retro_hsap_3407

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:177612761..177614300(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000244234
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GMCL1
Ensembl ID:ENSG00000087338
Aliases:None
Description:germ cell-less, spermatogenesis associated 1 [Source:HGNC Symbol;Acc:23843]


Retrocopy-Parental alignment summary:






>retro_hsap_3407
ATGGGATCGTCGAGCAGCCGGGTGCTGGGCCAGCCGAGGCGAGCCCTTGCCCAGCAGGAACAGGGTGCCAGGGCCAGGGG
CTCGGCCCGGAGGCCGGACACTGGAGACGATGCGGCGAGCTACGGCTTCTGTTACTGCCCGGGCAGTCACAAGCGCAAGC
GGAGCAGCGGGGCCTGCCGCTACTGTGACCCGGACTCGCACAGGGAGGAGCATGAGGAGGAGGGGGACAAGCAGCAGCCG
CTCCTCAACACCCCTGCAAGGAAAAAATTAAGGAGTACATCCAAATATATTTATCAAACATTATTTTTGAATGGTGAAAA
CAGTGACATTAAGATTTGTGCTCTAGGAGAAGAATGGCGATTACACAAAATATATTTATGTCAATCTGGCTACTTTTCTA
GTATGTTCAGTGGTTCTTGGAAAGAATCCAGCATGAATATTATTGAACTGGAGATTCCTGACCAGAACATTGATGTAGAC
GCACTGCAGGTTGCGTTTGGTTCACTGTATCGAGATGATGTCTTGATAAAACCCAGTCGAGTTGTTGCCATTTTGGCAGC
AGCTTGTATGCTGCAGCTGGATGGTTTAATACAGCAGTGTGGTGAGACAATGAAGGAAACAATTAATGTGAAAACTGTAT
GCGGTTATTACACATCAGTAGAGATCTATGGATTAGATTCTGTAAAGAAAAAGTGCCTTGAATGGCTTCTAAACAATTTG
ATGACTCACCAGAATGTTAAACTTTTTAAAGAACTCGGTATAAATGTCATGAAACAGCTCATTGGTTCCTCTAACTTATT
TGTGATGCAAGTGGAGATGGATGTATACACCACTCTAAAAAAGTGGATGTTCCTTCAACTTGTGCCTTCTTGGAATGGAT
CTTTAAAACAGCTTTTGACAGAAACAGATGTCTGGTTTTCTAAACAGAGAAAAGATTTTGAAGGTATGGCCTTTCTTGAA
ACTGAACCAGGAAAACCATTTGTGTCAGTATTCAGACATTTAAGGTTACAATATATTATCAGTGACCTAGCTTCTGCAAG
AATTATTGAACAAGATGGTATAGTACCTTCAGAATGGCTGTCTTCTGTGTATAAACAGCAGTGGTTTGCTATGCTGCGGG
CAGAACAAGACCGTGAGGTAGGGCCTCAAGAAATCAATAAAGAAGACCTAGAGGGAAATAGCATGAGGTGTGGTAGAAAG
CTTGCCAAAGATGGTGAATACTACTGGTGTTGGACGGGTTTTAACTTCGGCTTTGACCTACTTGTAATTTACACCAATGG
ATACATCATTTTCAAACGCAATACACTGAATCAGCCACGCAGCGGGTCTGTCAGTTTACGGCCTCGAAGGAGCATAGCAT
TTAGATTACGCTTGGCTTCTTTTGATAGTAGTGGAAAACTAGTATGTAGTAGAACAACTGGCTATCAAATACTTATACTT
AAAAAGGATCAGGAACAAGTGGTGATGAACTTGGACAGCAGGTTTCTGACCTTCCCTTTATATATCTGCTGTAACTTCTT
GTATATATCACCAGAAAAA

ORF - retro_hsap_3407 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.84 %
Parental protein coverage: 99.61 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGSLSSRVLRQPRPALAQQAQGARAGGSARRPDTGDDAAGHGFCYCAGSHKRKRSSGSFCYCHPDSETDE
MGS.SSRVL.QPR.ALAQQ.QGARA.GSARRPDTGDDAA..GFCYC.GSHKRKRSSG...YC.PDS...E
RetrocopyMGSSSSRVLGQPRRALAQQEQGARARGSARRPDTGDDAASYGFCYCPGSHKRKRSSGACRYCDPDSHREE
ParentalDEEEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSW
.EEEGD.QQ.LLNTP.RKKL.STSKYIYQTLFLNGENSDIKICALGEEW.LHKIYLCQSGYFSSMFSGSW
RetrocopyHEEEGDKQQPLLNTPARKKLRSTSKYIYQTLFLNGENSDIKICALGEEWRLHKIYLCQSGYFSSMFSGSW
ParentalKESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAACLLQLDGLIQQCGETMKETVNV
KESSMNIIELEIPDQNIDV.ALQVAFGSLYRDDVLIKPSRVVAILAAAC.LQLDGLIQQCGETMKET.NV
RetrocopyKESSMNIIELEIPDQNIDVDALQVAFGSLYRDDVLIKPSRVVAILAAACMLQLDGLIQQCGETMKETINV
ParentalKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSINVMKQLIGSSNLFVMQVEMDIYTALK
KTVCGYYTS...YGLDSVKKKCLEWLLNNLMTHQNV.LFKEL.INVMKQLIGSSNLFVMQVEMD.YT.LK
RetrocopyKTVCGYYTSVEIYGLDSVKKKCLEWLLNNLMTHQNVKLFKELGINVMKQLIGSSNLFVMQVEMDVYTTLK
ParentalKWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFEGMAFLETEQGKPFVSVFRHLRLQYIISDLASARIIE
KWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFEGMAFLETE.GKPFVSVFRHLRLQYIISDLASARIIE
RetrocopyKWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFEGMAFLETEPGKPFVSVFRHLRLQYIISDLASARIIE
ParentalQDAVVPSEWLSSVYKQQWFAMLRAEQDSEVGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDL
QD..VPSEWLSSVYKQQWFAMLRAEQD.EVGPQEINKE.LEGNSMRCGRKLAKDGEY.W.WTGFNFGFDL
RetrocopyQDGIVPSEWLSSVYKQQWFAMLRAEQDREVGPQEINKEDLEGNSMRCGRKLAKDGEYYWCWTGFNFGFDL
ParentalLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMN
LV.YTN.YIIFKRNTLNQP.SGSVSL.PRRSIAFRLRLASFDSSGKL.CSRTTGYQIL.L.KDQEQVVMN
RetrocopyLVIYTNGYIIFKRNTLNQPRSGSVSLRPRRSIAFRLRLASFDSSGKLVCSRTTGYQILILKKDQEQVVMN
ParentalLDSRLLIFPLYICCNFLYISPEK
LDSR.L.FPLYICCNFLYISPEK
RetrocopyLDSRFLTFPLYICCNFLYISPEK

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 .00 RPM 33 .43 RPM
bodymap2_adrenal 0 .00 RPM 12 .40 RPM
bodymap2_brain 0 .00 RPM 18 .49 RPM
bodymap2_breast 0 .00 RPM 26 .56 RPM
bodymap2_colon 0 .00 RPM 23 .88 RPM
bodymap2_heart 0 .00 RPM 11 .56 RPM
bodymap2_kidney 0 .00 RPM 31 .35 RPM
bodymap2_liver 0 .00 RPM 16 .67 RPM
bodymap2_lung 0 .00 RPM 19 .59 RPM
bodymap2_lymph_node 0 .00 RPM 28 .40 RPM
bodymap2_ovary 0 .00 RPM 26 .68 RPM
bodymap2_prostate 0 .00 RPM 38 .14 RPM
bodymap2_skeletal_muscle 0 .00 RPM 6 .00 RPM
bodymap2_testis 15 .84 RPM 51 .37 RPM
bodymap2_thyroid 0 .00 RPM 23 .78 RPM
bodymap2_white_blood_cells 0 .00 RPM 63 .65 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3407 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3407 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_1528511825 libraries1 library1 library2 libraries0 libraries

The graphical summary, for retro_hsap_3407 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_3407 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3407 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2314
Pongo abelii retro_pabe_209
Macaca mulatta retro_mmul_98
Parental genes homology:
Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG000000123062 retrocopies
retro_chof_1562, retro_chof_802,
Equus caballus ENSECAG000000168132 retrocopies
retro_ecab_1109, retro_ecab_899,
Homo sapiens ENSG00000087338 1 retrocopy
retro_hsap_3407 ,
Loxodonta africana ENSLAFG000000025653 retrocopies
retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG000000008581 retrocopy
retro_mmul_98,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG000000120211 retrocopy
retro_ptro_2314,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG000000007141 retrocopy
retro_itri_59,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,

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 = 0.03 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 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).





Copyright © RetrogeneDB 2014-2017