RetrogeneDB ID:

retro_hsap_3002

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:163244526..163245056(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251253
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MTHFD2
Ensembl ID:ENSG00000065911
Aliases:None
Description:methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Source:HGNC Symbol;Acc:7434]


Retrocopy-Parental alignment summary:






>retro_hsap_3002
CTACCAGCTCCTTCATAGGGTATGTGGGAAATGATGAAGTGAACTGGCATTCCAGCCCTAGAGAAGAATGTGATTGCAGC
TGGGAAATAAAAAAAATGTTGGGATGCTCATTTTAATGTTATTAAACACAGATGGGGCACATGAAAGTCCTGGAGGTGAT
GCCACGTTACAATATCTCATCAGTACACTCCCATAGAGCAGTTGAAGAAAAATATAATTCTTGCAGATATTGTAGTATCT
GCCTCAGGCATTCCAAATCTGATCACAGCAGATATCAAGGGAGGAGAAGCAATCATTGACATGAGAATACATAGAGTTCA
AGATCCCATAATTGCTAAACCCAAGTTGGTTGGAGATGTGGATTTTGAAGGAATCACGAAAAAGCTGATTACATCATTCC
AGTTCCTTGGGGTGTTCGTCCCAGGACAGTTGTGGTGTTAATGAAGAATATGATTATTACTGCCAAAACATTGTTGAGGC
CTGGAGAGCAGTAAGTGCTGAAGTCTAAAGAGCTTGTAGTAGCTACTCAT

ORF - retro_hsap_3002 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.96 %
Parental protein coverage: 71.77 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLPATPWGVWEIIKRTGIPTLGKNVVVAGRSKN-VGMPIAMLLHTDGAHERPGGDAT-VTISHRYTPKEQL
LPA...G.WE..K.TGIP.L.KNV..AG.....VGM.I.MLL.TDGAHE.PGGDAT.VTISH.YTP.EQL
RetrocopyLPAPS*GMWEMMK*TGIPALEKNVIAAGKXXX>VGMLILMLLNTDGAHESPGGDAT<VTISHQYTPIEQL
ParentalKKHTILADIVISAAGIPNLITADMIKEGAAVIDVGINRVHDPVTAKPKLVGDVDFEGV-RQKAGYITPVP
KK..ILADIV.SA.GIPNLITAD.IK.G.A.ID..I.RV.DP..AKPKLVGDVDFEG....KA.YI.PVP
RetrocopyKKNIILADIVVSASGIPNLITAD-IKGGEAIIDMRIHRVQDPIIAKPKLVGDVDFEGI<HEKADYIIPVP
ParentalGGVGPMTVAMLMKNTIIAAKKVLRLEEREVLKSKELGVATN
.GV.P.TV..LMKN.II.AK..LR..E..VLKSKEL.VAT.
RetrocopyWGVRPRTVVVLMKNMIITAKTLLRPGEQ*VLKSKELVVATH

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 50 .93 RPM
bodymap2_adrenal 0 .00 RPM 66 .94 RPM
bodymap2_brain 0 .00 RPM 25 .17 RPM
bodymap2_breast 0 .00 RPM 25 .91 RPM
bodymap2_colon 0 .00 RPM 92 .15 RPM
bodymap2_heart 0 .00 RPM 32 .51 RPM
bodymap2_kidney 0 .00 RPM 50 .44 RPM
bodymap2_liver 0 .00 RPM 2 .41 RPM
bodymap2_lung 0 .00 RPM 69 .83 RPM
bodymap2_lymph_node 0 .00 RPM 112 .66 RPM
bodymap2_ovary 0 .00 RPM 73 .56 RPM
bodymap2_prostate 0 .00 RPM 56 .41 RPM
bodymap2_skeletal_muscle 0 .00 RPM 126 .33 RPM
bodymap2_testis 0 .00 RPM 53 .07 RPM
bodymap2_thyroid 0 .00 RPM 49 .13 RPM
bodymap2_white_blood_cells 0 .00 RPM 46 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3002 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3002 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3002 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3002 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3002 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 10 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173452 retrocopies
retro_amel_1098, retro_amel_1584,
Canis familiaris ENSCAFG000000087161 retrocopy
retro_cfam_580,
Callithrix jacchus ENSCJAG000000178103 retrocopies
retro_cjac_2225, retro_cjac_2568, retro_cjac_3078,
Homo sapiens ENSG00000065911 5 retrocopies
retro_hsap_2732, retro_hsap_2817, retro_hsap_3002 , retro_hsap_3309, retro_hsap_3874,
Macropus eugenii ENSMEUG000000139874 retrocopies
retro_meug_1468, retro_meug_152, retro_meug_1577, retro_meug_2074,
Mustela putorius furoENSMPUG000000078293 retrocopies
retro_mputfur_1087, retro_mputfur_1397, retro_mputfur_1551,
Nomascus leucogenys ENSNLEG000000003265 retrocopies
retro_nleu_1196, retro_nleu_207, retro_nleu_2501, retro_nleu_595, retro_nleu_749,
Otolemur garnettii ENSOGAG000000090891 retrocopy
retro_ogar_3390,
Pan troglodytes ENSPTRG000000120814 retrocopies
retro_ptro_1846, retro_ptro_1910, retro_ptro_2162, retro_ptro_2641,
Pteropus vampyrus ENSPVAG000000139482 retrocopies
retro_pvam_1357, retro_pvam_1414,

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 ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 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 .00 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 .00 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 .00 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 .00 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 .00 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017