RetrogeneDB ID:

retro_hsap_3309

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:41967312..41968180(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000249266
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_3309
AATGAAGCTGTTGTCAGGAAACTGGCCCAGTGGATCAAGCAGGAAGTGCGGCAGGAGGTGGAGGAGCAGGTGGCCTCTGG
CAACAAAGGGCCATGCCTGAGCGTGGCTCTGGTCAGCAAAACTCCTGCAAGTCTCTGCCATATCCTCAACAAAACCAGGG
CAGCTGCAGATGTGGGAATCAACAGTGAGATAATTGTGAAACCAGCTTCAATTTCAGAGGAAGAATTGTTGAATTTAATC
AATAAATTGAATAATGATGGTAATGTAGATGGCCTCCTTCTCCACCTGCCTCTTCCAGAGCACATTGATGAGAGAAAGAT
CTGCAATTCTGTTTTTCCAGATAAGGATGTTGATGGCTTTCATGTAATTAATGTAGGGTGAATGTATCTGGACCAGTATT
CCGTATACCAGCTACTCCATGCAGTGTGTGGGAAATAATTAAGCAAACTGGCATTCCAACCCTAGGGAAGAATGTGGTTG
TGGCTGGAAGGTCAAAAAATGTTGTAATGCCTATTGCAATGTCACTGCACACAGATGGGGTGCATGAACGTCACGGAGGT
GATGCCACTGTTATAATATCTCATTGATATACCCCCAAAGAGCAGTTGAGGAAACATACAATTCTTGCAGATATTGTAAT
ATCTGTTGCAGGTGTTCCAAATCTGATCACAGCAAATATGACCAAGGGAGAAGCAATAGCATTGATGTGGGAATAGATAC
AGTTCAAGATCCTGTAACTGCTAAACCTAAGTTGGTTGGAAATGTGGATTTTAAAGGAGTTAGGCAAAAAGCCAGTTATA
TCACTCCAGTTTCTGGAGGTGTTGGCCCTATGACAGTGGCAATGCTAATGAAGAATACCATAATTGCC

ORF - retro_hsap_3309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.36 %
Parental protein coverage: 83.71 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNEAVVISGRKLAQQIKQEVRQEVEEWVASGNKRPHLSVILVGENPASHSYVLNKTRAAAVVGINSETIMK
NEAVV...RKLAQ.IKQEVRQEVEE.VASGNK.P.LSV.LV...PAS....LNKTRAAA.VGINSE.I.K
RetrocopyNEAVV---RKLAQWIKQEVRQEVEEQVASGNKGPCLSVALVSKTPASLCHILNKTRAAADVGINSEIIVK
ParentalPASISEEELLNLINKLNNDDNVDGLLVQLPLPEHIDERRICNAVSPDKDVDGFHVINVGRMCLDQYSM-L
PASISEEELLNLINKLNND.NVDGLL..LPLPEHIDER.ICN.V.PDKDVDGFHVINVG.M.LDQYS...
RetrocopyPASISEEELLNLINKLNNDGNVDGLLLHLPLPEHIDERKICNSVFPDKDVDGFHVINVG*MYLDQYSV<I
ParentalPATPWGVWEIIKRTGIPTLGKNVVVAGRSKNVGMPIAMLLHTDGAHERPGGDATVTISHRYTPKEQLKKH
PATP..VWEIIK.TGIPTLGKNVVVAGRSKNV.MPIAM.LHTDG.HER.GGDATV.ISH.YTPKEQL.KH
RetrocopyPATPCSVWEIIKQTGIPTLGKNVVVAGRSKNVVMPIAMSLHTDGVHERHGGDATVIISH*YTPKEQLRKH
ParentalTILADIVISAAGIPNLITADMIKEGAAV-IDVGINRVHDPVTAKPKLVGDVDFEGVRQKAGYITPVPGGV
TILADIVIS.AG.PNLITA.M.K..A...IDVGI..V.DPVTAKPKLVG.VDF.GVRQKA.YITPV.GGV
RetrocopyTILADIVISVAGVPNLITANMTKGEAIA<IDVGIDTVQDPVTAKPKLVGNVDFKGVRQKASYITPVSGGV
ParentalGPMTVAMLMKNTIIA
GPMTVAMLMKNTIIA
RetrocopyGPMTVAMLMKNTIIA

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 .06 RPM 25 .91 RPM
bodymap2_colon 0 .00 RPM 92 .15 RPM
bodymap2_heart 0 .04 RPM 32 .51 RPM
bodymap2_kidney 0 .12 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 .07 RPM 126 .33 RPM
bodymap2_testis 0 .02 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_3309 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3309 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3309 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3309 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3309 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2162
Pongo abelii retro_pabe_2729
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 ) > 0 RPM = 0.04 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 .04 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 .02 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 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 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).



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