RetrogeneDB ID:

retro_hsap_4839

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:57419078..57421071(-)
Located in intron of:ENSG00000165591
Retrocopy
information
Ensembl ID:ENSG00000231831
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MTHFD1
Ensembl ID:ENSG00000100714
Aliases:MTHFD1, MTHFC, MTHFD
Description:methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase [Source:HGNC Symbol;Acc:7432]


Retrocopy-Parental alignment summary:






>retro_hsap_4839
CCCGTTCCTGGTGGCTTAGGGCTCATGACGGTTGCAATGCTCATGCAGAGCACTGTAGAGAGTGCCAAGCGTTTCCTGGA
GAAATTTAAGCCAGGAAAGTGGATGATTCAGTATAACAACCTTAACCTCAAGACACCTGTTCCAAGTGACATTGATATAT
CACGATCTTGTAAACCGAAGCCCATTGGTAAGCTGGCTTGAGTAATTGGTCTGCTGTCTGAAGAGGTAGAATTATATGGT
GAAACAAAGGCCAAAGTTCTGCTGTCAGCACTAGAACGCCTGAAGCACCAGCCTGTTGGGAAATATCAGGTGGTGACTGG
AATAACTCCAACACCCCTGGGAGAAGGGAAAAGCACGACTACAATCGGGCTGGTGCAAGCCCTTCTTGCCCATCTTTACC
AGAACTTTTTTATGTGTGTGCGACAGCCTTCTCAGGGCCCCACCTTTGGAATAAAAGGTGGTGTTGCAGGAGGCGGCTAC
TCCCAGGTCATTCCTATGGAAGAGTTTAATCTTCACCTCACAGGTGACATCCATGCCATCACTGTATCTAATAACCTTGT
TGCTGCGGCTATTGATGCTCAGATATTTCATGAACTGACCCAGACAGACAAGGCTACCTTTACTCATTTGGTGCCATCAG
TAAATGGAGTGAGAAAGTTCTCTGATATCCACATACAAAGGTTAAACAGACTAGGCATTGACAAGACTGACTCTACCACA
CTGACAGATGAAGAGATAAACAGATTTGCAAGATTGGACATTGATCCAGAAACCATAGCTTGGCAAAGAGTGTTGAATAC
CAATGATAGATTCCTGAGGAAGATCACGATTGGACAGGCTCCAACGAAGAAAAGTCACACACAGACGGTCCACTTTGATA
TCTCTGTGGCCAGTGAAATTATGGCTGTCCTGGCTCTCACCACTTCTCTAGAAGACAGGAGAGAGAGACTGGGCAAAATG
GTGGTGGCATCCAGTAAGAAAGGAGACCCCGTCAGTGCTGAAGATCTGGGGGTGAGTGGTGCATTGATAGTGCTTATGAA
GGACACAATCAAGCCCAATCTCATGCAGAGATTGGAGGGCACTCCAGTGTTTGTCCATGCAGGCCCATTTGCCATCATCG
CACACGGCAATTCCTCTATCATTGCAGACCGGATCACACTCTAGCTTGTTGGCCCAGAAGGGTTTGTAGTGACGGAGGCG
GGATTTGGAGCAGACATTGGAATAGAAAAGTTTCTTAACATCAAATCCCAGTATTCCGGTCTCCACCCTCACGTGGTGGT
GCTTGTTGCCACTGTCAGCGCTCTAAAGATGCACAGGGGTGGCCCTATGGTCACTGCTGGAATGCCTCTTCCCAAGGCTT
ACATAGAGGAGAACCTGGAGCTGGTTGAAAAAGGCTTCAGTAACTTGAAGAAACAAACTGAAAATGCCAGAATGTTTGGA
ATTCCAGTAGTAGTGGCCGTGAATGCATTCAAGACAGATACAGAGACTGAGCTGGACCTCATCGGCTGCCTTTCCAGAGA
ACAGAGGGCTTTTGATGCCGTGAAGTGCACTCACTGGCAGAAGGGGGCAAGGGTACCTTAGCCCTGGCTCAGGCTGTCCA
GAGAGCAGGACAAGCACCCAGCAGCTTCCAACTCCTTTATGACCTCAAGCTCCCAGTTGAGGATAAAATCAGGATCATTG
CACAGAAGATCTATGGAGCAGACAACATTGAATTACTCCTCAAAGCTCAACACAAAGCTGAAGTCTACACAAAGCAGGGC
TTTGGGAATCTCCCCATCTGCATGGCCAAAACACACTTGTCCTTGTCTCACAACCCAGAGCGAAAAGGTGTCCCTACAGG
ATTCATTCTGCCCATTCGCAACATCCATGCCAGCATCGGGGCTGGTTTTCTGTACCCTTTAGTAGGAACGATGAGCACAA
TGGACTCCCCACCCAGCCCTGTTTTTATGATACTGATTTGGACCCTGAAACAGAACAGGTGAATGGATCATTC

ORF - retro_hsap_4839 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.07 %
Parental protein coverage: 67.2 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPVPGGVGPMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCKPKPIGKLAREIG
PVPGG.G.MTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCKPKPIGKLA..IG
RetrocopyPVPGGLGLMTVAMLMQSTVESAKRFLEKFKPGKWMIQYNNLNLKTPVPSDIDISRSCKPKPIGKLA*VIG
ParentalLLSEEVELYGETKAKVLLSALERLKHRPDGKYVVVTGITPTPLGEGKSTTTIGLVQALGAHLYQNVFACV
LLSEEVELYGETKAKVLLSALERLKH.P.GKY.VVTGITPTPLGEGKSTTTIGLVQAL.AHLYQN.F.CV
RetrocopyLLSEEVELYGETKAKVLLSALERLKHQPVGKYQVVTGITPTPLGEGKSTTTIGLVQALLAHLYQNFFMCV
ParentalRQPSQGPTFGIKGGAAGGGYSQVIPMEEFNLHLTGDIHAITAANNLVAAAIDARIFHELTQTDKALFNRL
RQPSQGPTFGIKGG.AGGGYSQVIPMEEFNLHLTGDIHAIT..NNLVAAAIDA.IFHELTQTDKA.F..L
RetrocopyRQPSQGPTFGIKGGVAGGGYSQVIPMEEFNLHLTGDIHAITVSNNLVAAAIDAQIFHELTQTDKATFTHL
ParentalVPSVNGVRRFSDIQIRRLKRLGIEKTDPTTLTDEEINRFARLDIDPETITWQRVLDTNDRFLRKITIGQA
VPSVNGVR.FSDI.I.RL.RLGI.KTD.TTLTDEEINRFARLDIDPETI.WQRVL.TNDRFLRKITIGQA
RetrocopyVPSVNGVRKFSDIHIQRLNRLGIDKTDSTTLTDEEINRFARLDIDPETIAWQRVLNTNDRFLRKITIGQA
ParentalPTEKGHTRTAQFDISVASEIMAVLALTTSLEDMRERLGKMVVASSKKGEPVSAEDLGVSGALTVLMKDAI
PT.K.HT.T..FDISVASEIMAVLALTTSLED.RERLGKMVVASSKKG.PVSAEDLGVSGAL.VLMKD.I
RetrocopyPTKKSHTQTVHFDISVASEIMAVLALTTSLEDRRERLGKMVVASSKKGDPVSAEDLGVSGALIVLMKDTI
ParentalKPNLMQTLEGTPVFVHAGPFANIAHGNSSIIADRIALKLVGPEGFVVTEAGFGADIGMEKFFNIKCRYSG
KPNLMQ.LEGTPVFVHAGPFA.IAHGNSSIIADRI.L.LVGPEGFVVTEAGFGADIG.EKF.NIK..YSG
RetrocopyKPNLMQRLEGTPVFVHAGPFAIIAHGNSSIIADRITL*LVGPEGFVVTEAGFGADIGIEKFLNIKSQYSG
ParentalLCPHVVVLVATVRALKMHGGGPTVTAGLPLPKAYIQENLELVEKGFSNLKKQIENARMFGIPVVVAVNAF
L.PHVVVLVATV.ALKMH.GGP.VTAG.PLPKAYI.ENLELVEKGFSNLKKQ.ENARMFGIPVVVAVNAF
RetrocopyLHPHVVVLVATVSALKMHRGGPMVTAGMPLPKAYIEENLELVEKGFSNLKKQTENARMFGIPVVVAVNAF
ParentalKTDTESELDLISRLSREHGAFDAVKCTHW-AEGGKGALALAQAVQRAAQAPSSFQLLYDLKLPVEDKIRI
KTDTE.ELDLI..LSRE..AFDAVKCTHW.AEGGKG.LALAQAVQRA.QAPSSFQLLYDLKLPVEDKIRI
RetrocopyKTDTETELDLIGCLSREQRAFDAVKCTHW<AEGGKGTLALAQAVQRAGQAPSSFQLLYDLKLPVEDKIRI
ParentalIAQKIYGADDIELLPEAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPEQKGVPTGFILPIRDIRASVGAG
IAQKIYGAD.IELL..AQHKAEVYTKQGFGNLPICMAKTHLSLSHNPE.KGVPTGFILPIR.I.AS.GAG
RetrocopyIAQKIYGADNIELLLKAQHKAEVYTKQGFGNLPICMAKTHLSLSHNPERKGVPTGFILPIRNIHASIGAG
ParentalFLYPLVGTMSTMPGLPTRPCF-YDIDLDPETEQVNGLF
FLYPLVGTMSTM...P..P.F.YD.DLDPETEQVNG.F
RetrocopyFLYPLVGTMSTMDS-PPSPVF<YDTDLDPETEQVNGSF

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 .14 RPM 98 .22 RPM
bodymap2_adrenal 0 .00 RPM 46 .20 RPM
bodymap2_brain 0 .00 RPM 53 .14 RPM
bodymap2_breast 0 .04 RPM 128 .27 RPM
bodymap2_colon 0 .00 RPM 42 .87 RPM
bodymap2_heart 0 .00 RPM 49 .64 RPM
bodymap2_kidney 0 .14 RPM 65 .62 RPM
bodymap2_liver 0 .00 RPM 213 .77 RPM
bodymap2_lung 0 .16 RPM 31 .68 RPM
bodymap2_lymph_node 0 .15 RPM 35 .82 RPM
bodymap2_ovary 0 .04 RPM 68 .16 RPM
bodymap2_prostate 0 .23 RPM 49 .21 RPM
bodymap2_skeletal_muscle 0 .02 RPM 153 .40 RPM
bodymap2_testis 0 .00 RPM 33 .82 RPM
bodymap2_thyroid 0 .02 RPM 72 .39 RPM
bodymap2_white_blood_cells 0 .10 RPM 27 .78 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4839 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4839 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4839 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4839 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4839 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3223
Gorilla gorilla retro_ggor_3018
Parental genes homology:
Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000159671 retrocopy
retro_cfam_300,
Homo sapiens ENSG00000100714 1 retrocopy
retro_hsap_4839 ,
Gorilla gorilla ENSGGOG000000052511 retrocopy
retro_ggor_3018,
Microcebus murinus ENSMICG000000130116 retrocopies
retro_mmur_1069, retro_mmur_1250, retro_mmur_1462, retro_mmur_451, retro_mmur_777, retro_mmur_993,
Macaca mulatta ENSMMUG000000013191 retrocopy
retro_mmul_2583,
Pan troglodytes ENSPTRG000000064351 retrocopy
retro_ptro_3223,

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 = 0.28 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .09 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .14 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .14 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .14 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .14 RPM
TSI_NA20513 0 .15 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .08 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .12 RPM

Indel association:

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





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