General information for g2415.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glutamate [NMDA] receptor subunit 1.
Parent gene
- The parent gene g2415 is located on chr_3: 17838568..17854436 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g2415 | g2415.t1 | isoform | g2415.t1 | 17838568 | 17854436 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon1 | 17838568 | 17838735 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS1 | 17838568 | 17838735 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon2 | 17841860 | 17842210 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS2 | 17841860 | 17842210 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon3 | 17842750 | 17842952 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS3 | 17842750 | 17842952 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon4 | 17846474 | 17846636 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS4 | 17846474 | 17846636 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon5 | 17847441 | 17847605 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS5 | 17847441 | 17847605 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon6 | 17847700 | 17847801 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS6 | 17847700 | 17847801 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon7 | 17848243 | 17848459 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS7 | 17848243 | 17848459 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon8 | 17849594 | 17849674 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS8 | 17849594 | 17849674 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon9 | 17849933 | 17850260 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS9 | 17849933 | 17850260 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon10 | 17850590 | 17851018 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS10 | 17850590 | 17851018 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon11 | 17851114 | 17851286 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS11 | 17851114 | 17851286 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon12 | 17851356 | 17851408 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS12 | 17851356 | 17851408 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon13 | 17851481 | 17851571 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS13 | 17851481 | 17851571 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon14 | 17851771 | 17851880 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS14 | 17851771 | 17851880 |
| chr_3 | g2415 | g2415.t1 | exon | g2415.t1.exon15 | 17854161 | 17854436 |
| chr_3 | g2415 | g2415.t1 | cds | g2415.t1.CDS15 | 17854161 | 17854436 |
| chr_3 | g2415 | g2415.t1 | TSS | g2415.t1 | NA | NA |
| chr_3 | g2415 | g2415.t1 | TTS | g2415.t1 | NA | NA |
Sequences
>g2415.t1 Gene=g2415 Length=2910
ATGTGGCACAAAATTAGTGAATTCTATTTATGGACACTGTTGCTGTTTACGTTCAACAAT
TATGTTCTCTTACAAAAGCCTAATAGCAGCGATAATCCCTCTTTCTTTAATATCGGCGGC
GTATTAAGCAATAGTGAAAGCGAGAAAAATTTTTCCGATACAATAGCTACATTGAATTAT
GTACAAGCGTATGTGCCACGAGGAACAACTTATTATGATAAAACAATACGAATAGATAAG
AATCCCATTAAAACAGCTTTAAATGTTTGCAAACATCTTATATCGAAGCGGGTGTATGCG
GTTGTGGTGTCGCATGACGACTCATCGGGGCATGATTTATCGCCAGCTGCTGTGAGTTAT
ACGAGTGGCTTCTATCAGATACCAGTCATAGGGATTTCATCGCGTGACGCAGCATTTTCT
GATAAGAATATTCATGTTTCTTTCTTGAGGACAGTGCCGCCATACTATCATCAAGCGGAC
GTATGGCTTGAAATGCTTAGTCATTTTGGATACACAAAGGTGATTATAATTCACAGTTCT
GACACTGACGGTCGAGCGATTTTAGGCCGCTTTCAGACAACATCGCAAACAAATTACGAC
GATATTGATGTTCGTGCAAATGTTGAGTCAATTGTAGAATTTGAGCCAAAGTTGGAAAGT
TTTACTGAATATTTATCGGAATTGAAGTCAGCACAGTCTCGCGTTTATCTATTATATGCA
AATAAGGACGATGCCTTTACAATTTTTCGAGATGCGGCTGTTGAAAATATGACAGAAGCG
GGTCATGTTTGGATTGTAACAGAACAGGCGTTGCTCGCTAACAACACACCCATTGGAACA
TTGGGCCTTAAGCTGAATAACGACAATGAATCGGATCATATCAGAGATAGTGTCTATGTA
TTGGCACATGCACTAAAGGATATGCTACTGAATGAGTCGATTACGGAAGCGCCGAAAGAC
TGCGATGACTCAGGCGTCTTCTGGGAGACAGGCCGGAAGCTTTTTCACTACTTGAAGTCG
CGTAACATCAACGGCAAAACGGGTCGAGTGGCCTTCGATGACTCCGGCGATAGAATAAAT
GCCGAATATGATGTAATAAATATTGGTAAAAAAGGTGGAATGAAAGTTGTTGGTAGCTTC
TTTTTTGATAATGAAAAGGAAAAAATGCGTTTAAAAATCAATGATAGTGAAATAATTTGG
CCTGGTAAAGTGAAAAAGAAACCGGAAGGATTCTTTATACCAACACATTTGAAGGTGCTA
ACAATTGAAGAAAAACCTTTTGTCTATGTACGAAAAGTAACAGAAGAAAATCCGGAATGT
GAGGATGATGAAATTGAGTGCCCGCTCTTTAATAAAACTGATGGAAATGAAAAGGATTAT
TGCTGTCGTGGATATTGCATAGATTTGCTTAAAGCATTATCACATCGCATTAATTTCACA
TACGATTTGGCATTATCGCCTGATGGTCAATTTGGTCATTACATAATCAAAAACTTGTCC
AGCACAATGGGAGTGAAAAAAGAATGGACAGGACTGATCGGTGAGCTCGTTGCTGAGCGA
GCTGATTTAATTGTCGCACCATTGACAATTAACCCAGAAAGAGCCGAATTCATTGAATTC
TCGAAACCGTTTAAATACCAGGGCATTACGATATTGGAAAAGAAGCCATCACGAAGTTCG
ACTCTCGTGAGTTTCTTGCAACCATTCAGCAATACCCTGTGGATTCTCGTTATGGTTTCG
GTTCATGTTGTGGCTCTAGTTCTCTATCTGCTGGATAGATTTTCGCCCTTTGGCCGTTTT
AAGCTGTTAAACAACGATGGAACAGAGGAAGATGCTTTAAATTTGAGTTCAGCTATTTGG
TTTGCATGGGGTGTGCTGTTAAATAGTGGCATAGGTGAAGGAACACCAAGAAGTTTTTCA
GCTCGCGTGCTCGGCATGGTTTGGGCTGGTTTTGCAATGATCATTGTTGCTTCATATACT
GCCAACCTCGCTGCCTTTCTCGTCTTGGAGCGACCAAAAACTAAACTTTCGGGTATAAAT
GACGCACGTCTGCGTAATACAATGGAAAATTTGACGTGTGCAACAGTGAAGGGCTCAGCT
GTTGACATGTATTTCCGTCGACAAGTGGAGCTTTCAAATATGTACAGAACGATGGAAGCG
AACAACTATGATACTGCTGAACAGGCTATTCAGGATGTAAAAGACGGCAAACTGATGGCA
TTTATTTGGGATTCATCACGACTCGAGTATGAAGCGGCAAAAGATTGTGAACTTGTAACT
GCTGGTGAATTATTTGGACGAAGTGGTTATGGAATTGGTCTACAAAAAGGAAGTCCTTGG
ACGGACGCTGTTACATTAGCTATTTTAGATTTTCACGAAAGTGGTTTTATGGAAGCATTA
GATAAAGAATGGATTTTCCATGGGAATATCCAGCAATGCGAACAATTTGAGAAAACGCCA
AATACACTAGGCCTGAAGAATATGGCTGGCGTTTTTATATTGGTCGGCGCGGGAATTATT
GGAGGCGTTGGTCTGATAATTATTGAAGTTGTATATAAAAAGCATCAAATAAAGAAACAG
AAGCGAATGGAAATCGCCAGACATGCGGCAGACAAATGGAGAGGAACAATTGAGAAACGG
AAGCACCTTCGTCAGTCGCTTGCAATGCAAAGACAGTATAATGTGGGTCTTAATTCAGTC
ACGAAATCAATTAGTCAGGCCGTCGACAAAAATCGTTACCCGACAATGGGATGGAATACA
GGCGCGCTGTCGGCACAAGATTTGTCAATGGGCCGACATCGACTGAACGGTGATGAGTAC
AGTATCTATAATAATCGACATAAAAAGCCACCTAAACACAAGCCATCTATACCAACATAC
GCTTCAGATGTATCTCATTTGGTTGTTTAA
>g2415.t1 Gene=g2415 Length=969
MWHKISEFYLWTLLLFTFNNYVLLQKPNSSDNPSFFNIGGVLSNSESEKNFSDTIATLNY
VQAYVPRGTTYYDKTIRIDKNPIKTALNVCKHLISKRVYAVVVSHDDSSGHDLSPAAVSY
TSGFYQIPVIGISSRDAAFSDKNIHVSFLRTVPPYYHQADVWLEMLSHFGYTKVIIIHSS
DTDGRAILGRFQTTSQTNYDDIDVRANVESIVEFEPKLESFTEYLSELKSAQSRVYLLYA
NKDDAFTIFRDAAVENMTEAGHVWIVTEQALLANNTPIGTLGLKLNNDNESDHIRDSVYV
LAHALKDMLLNESITEAPKDCDDSGVFWETGRKLFHYLKSRNINGKTGRVAFDDSGDRIN
AEYDVINIGKKGGMKVVGSFFFDNEKEKMRLKINDSEIIWPGKVKKKPEGFFIPTHLKVL
TIEEKPFVYVRKVTEENPECEDDEIECPLFNKTDGNEKDYCCRGYCIDLLKALSHRINFT
YDLALSPDGQFGHYIIKNLSSTMGVKKEWTGLIGELVAERADLIVAPLTINPERAEFIEF
SKPFKYQGITILEKKPSRSSTLVSFLQPFSNTLWILVMVSVHVVALVLYLLDRFSPFGRF
KLLNNDGTEEDALNLSSAIWFAWGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYT
ANLAAFLVLERPKTKLSGINDARLRNTMENLTCATVKGSAVDMYFRRQVELSNMYRTMEA
NNYDTAEQAIQDVKDGKLMAFIWDSSRLEYEAAKDCELVTAGELFGRSGYGIGLQKGSPW
TDAVTLAILDFHESGFMEALDKEWIFHGNIQQCEQFEKTPNTLGLKNMAGVFILVGAGII
GGVGLIIIEVVYKKHQIKKQKRMEIARHAADKWRGTIEKRKHLRQSLAMQRQYNVGLNSV
TKSISQAVDKNRYPTMGWNTGALSAQDLSMGRHRLNGDEYSIYNNRHKKPPKHKPSIPTY
ASDVSHLVV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 36 | g2415.t1 | CDD | cd06379 | PBP1_iGluR_NMDA_NR1 | 34 | 402 | 1.03849E-178 |
| 35 | g2415.t1 | CDD | cd13719 | PBP2_iGluR_NMDA_Nr1 | 414 | 814 | 6.25975E-176 |
| 21 | g2415.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 37 | 363 | 1.1E-145 |
| 20 | g2415.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 154 | 402 | 1.1E-145 |
| 18 | g2415.t1 | Gene3D | G3DSA:3.40.190.10 | - | 462 | 820 | 4.8E-116 |
| 19 | g2415.t1 | Gene3D | G3DSA:3.40.190.10 | - | 548 | 770 | 4.8E-116 |
| 17 | g2415.t1 | Gene3D | G3DSA:1.10.287.70 | - | 558 | 849 | 4.8E-116 |
| 6 | g2415.t1 | PANTHER | PTHR18966 | IONOTROPIC GLUTAMATE RECEPTOR | 37 | 872 | 4.1E-226 |
| 7 | g2415.t1 | PANTHER | PTHR18966:SF497 | GLUTAMATE RECEPTOR, IONOTROPIC, N-METHYL D-ASPARTATE 1B | 37 | 872 | 4.1E-226 |
| 10 | g2415.t1 | PRINTS | PR00177 | NMDA receptor signature | 479 | 507 | 2.1E-58 |
| 9 | g2415.t1 | PRINTS | PR00177 | NMDA receptor signature | 573 | 598 | 2.1E-58 |
| 8 | g2415.t1 | PRINTS | PR00177 | NMDA receptor signature | 612 | 636 | 2.1E-58 |
| 11 | g2415.t1 | PRINTS | PR00177 | NMDA receptor signature | 643 | 670 | 2.1E-58 |
| 12 | g2415.t1 | PRINTS | PR00177 | NMDA receptor signature | 828 | 852 | 2.1E-58 |
| 2 | g2415.t1 | Pfam | PF01094 | Receptor family ligand binding region | 79 | 270 | 7.7E-27 |
| 3 | g2415.t1 | Pfam | PF01094 | Receptor family ligand binding region | 296 | 369 | 1.1E-14 |
| 5 | g2415.t1 | Pfam | PF10613 | Ligated ion channel L-glutamate- and glycine-binding site | 416 | 556 | 6.4E-33 |
| 1 | g2415.t1 | Pfam | PF00060 | Ligand-gated ion channel | 571 | 839 | 1.6E-37 |
| 4 | g2415.t1 | Pfam | PF10562 | Calmodulin-binding domain C0 of NMDA receptor NR1 subunit | 850 | 878 | 3.6E-16 |
| 27 | g2415.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 28 | g2415.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 29 | g2415.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 18 | - |
| 34 | g2415.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 24 | - |
| 25 | g2415.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 572 | - |
| 31 | g2415.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 573 | 591 | - |
| 22 | g2415.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 592 | 611 | - |
| 30 | g2415.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 612 | 631 | - |
| 26 | g2415.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 632 | 642 | - |
| 32 | g2415.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 643 | 669 | - |
| 23 | g2415.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 670 | 827 | - |
| 33 | g2415.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 828 | 852 | - |
| 24 | g2415.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 853 | 969 | - |
| 41 | g2415.t1 | SMART | SM00079 | GluR_14 | 416 | 807 | 2.2E-85 |
| 40 | g2415.t1 | SMART | SM00918 | Lig_chan_Glu_bd_2 | 448 | 518 | 3.3E-19 |
| 14 | g2415.t1 | SUPERFAMILY | SSF53822 | Periplasmic binding protein-like I | 78 | 410 | 2.05E-57 |
| 15 | g2415.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 416 | 805 | 1.19E-50 |
| 13 | g2415.t1 | SUPERFAMILY | SSF81324 | Voltage-gated potassium channels | 572 | 673 | 2.49E-8 |
| 16 | g2415.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
| 39 | g2415.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 572 | 591 | - |
| 38 | g2415.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 647 | 669 | - |
| 37 | g2415.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 830 | 852 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0038023 | signaling receptor activity | MF |
| GO:0016020 | membrane | CC |
| GO:0015276 | ligand-gated ion channel activity | MF |
| GO:0005216 | ion channel activity | MF |
| GO:0004970 | ionotropic glutamate receptor activity | MF |
| GO:0006811 | ion transport | BP |
KEGG
Orthology
- This transcript has been annotated with K05208 (glutamate receptor ionotropic, NMDA 1)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
