General information for g3564.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glutamate dehydrogenase, mitochondrial.
Parent gene
- The parent gene g3564 is located on chr_3: 26458192..26459186 (+ 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 | g3564 | g3564.t1 | TSS | g3564.t1 | 26453991 | 26453991 |
| chr_3 | g3564 | g3564.t1 | isoform | g3564.t1 | 26454100 | 26459067 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon1 | 26454100 | 26454270 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS1 | 26454100 | 26454270 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon2 | 26454356 | 26454593 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS2 | 26454356 | 26454593 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon3 | 26456961 | 26457028 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS3 | 26456961 | 26457028 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon4 | 26457089 | 26457467 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS4 | 26457089 | 26457467 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon5 | 26457548 | 26457561 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS5 | 26457548 | 26457561 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon6 | 26457630 | 26457818 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS6 | 26457630 | 26457818 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon7 | 26457879 | 26458188 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS7 | 26457879 | 26458188 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon8 | 26458419 | 26458457 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS8 | 26458419 | 26458457 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon9 | 26458735 | 26458884 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS9 | 26458735 | 26458884 |
| chr_3 | g3564 | g3564.t1 | exon | g3564.t1.exon10 | 26458946 | 26459067 |
| chr_3 | g3564 | g3564.t1 | cds | g3564.t1.CDS10 | 26458946 | 26459067 |
| chr_3 | g3564 | g3564.t1 | TTS | g3564.t1 | 26459449 | 26459449 |
Sequences
>g3564.t1 Gene=g3564 Length=1680
ATGTTTCACTTGAAGAAAATTATTAAATCACCATTAGTTAATCCAAAAGAGTTGTCACGC
GTTCTGCCAATTGCATTCAATAATCAATCATGTCGCGATTATTCCGGTCATCAAATTCCA
GAACGTTTGCAGTCTGTTCCTACAGACACAAATCCAAAATTCTTTGATATGGTTGAATAT
TTCTATCACCGTGGATGTCAAGTTGTTGAGGATTCCTTGGTGGAAAATATGAAGGAACGT
GCTACACTTGAAGAAAAACGTCATAAAGTTAGAGGAATTTTAATGCTCATGCAAACTTGC
GACCATATTATTGAAATTACCTTCCCTCTTCGTCGTGATAATGGAGTTTATGAGCTCATC
ACTGGCTATCGTGCTCAACATTCAACACATCGTACTCCAACTAAAGGAGGTATTCGTTTT
TCAATGGATGTCTCCCGTGATGAAGTAAAAGCCTTATCTGCATTGATGACATTTAAGTGT
GCTTGTGTCGACGTTCCATTTGGAGGAGCAAAGGCTGGAATCAGAATTAATCCGAAAGAA
TACTCAGAACATGAGTTAGAAAAGATTACACGTCGTTTTGCCCTTGAATTAGCAAAGAAA
GGATTTATCGGACCAGGAGTCGATGTTCCTGCACCCGATATGGGAACTGGAGAACGCGAA
ATGAGCTGGATTGCTGACACATATGCAAAGACCATTGGATATCAAGATATTAACGCACAT
GCTTGTATCACTGGTAAACCAATTAATCAAGGAGGTATTCATGGAAGAGTTTCTGCTACA
GGTCGTGGAGTGTTCCATGGTCTCGAGAATTTTATTAATGAAGCATCATATATGAGTCAA
ATTGGAACAACGCCTGGATGGGGTGGCAAGACATTTGTTGTGCAAGGTTTTGGTAATGTC
GGTCTTCATACATGTCGCTATTTGACACGAGCTGGAGCTACATGCATTGGAATCATTGAA
CATGATGGATCAATTTATAATCCACAAGGTATTGACCCCAAAGCACTCGAGGATTATAGA
ATTGAACACGGAACTATTGTTGGCTTTCCAGGAGCTAAACCATATGAAGGCGAAAGTTTA
ATGTATGAAGAATGTGACATTTTTGTACCAGCTGCTATTGAAAAGGTTATTACAAGTGAA
AATGCTCATAAAATCAAAGCAAAAATTATTGCTGAAGCTGCCAACGGTCCAACAACTCCA
GCTGCAGATAAAATATTGATCGATCGTAATATCCTTGTCATTCCTGATCTTTACATAAAC
GCTGGTGGTGTGACAGTTTCATTCTTTGAATGGCTTAAAAATCTTAATCATGTTTCATAT
GGACGTTTAACATTTAAATATGAACGTGAATCAAACTATCACTTATTAGCTTCAATTGAA
GAATCTCTTGATAAGGCTCTAAATGACAAAAGTGTACAAGAATCTTTGGAACGCAGATTC
GGTCGTGTAGGTGGAAAAATTCCAGTGACGCCTTCAGAAGCTTTCCAAAAAAGAATTTCA
GGTGCATCTGAAAAAGATATTGTTCACTCTGGTCTTGATTATACAATGGAAAGATCAGCA
CGCGCAATAATGAGAACTGCAACACGTTTCAATCTTGGTCTTGATCTGAGAACTGCTGCT
TATGTCAACTCAATCGAGAAAATTTTCACAACCTATCGTGATGCTGGCTTGGCTTTTTAA
>g3564.t1 Gene=g3564 Length=559
MFHLKKIIKSPLVNPKELSRVLPIAFNNQSCRDYSGHQIPERLQSVPTDTNPKFFDMVEY
FYHRGCQVVEDSLVENMKERATLEEKRHKVRGILMLMQTCDHIIEITFPLRRDNGVYELI
TGYRAQHSTHRTPTKGGIRFSMDVSRDEVKALSALMTFKCACVDVPFGGAKAGIRINPKE
YSEHELEKITRRFALELAKKGFIGPGVDVPAPDMGTGEREMSWIADTYAKTIGYQDINAH
ACITGKPINQGGIHGRVSATGRGVFHGLENFINEASYMSQIGTTPGWGGKTFVVQGFGNV
GLHTCRYLTRAGATCIGIIEHDGSIYNPQGIDPKALEDYRIEHGTIVGFPGAKPYEGESL
MYEECDIFVPAAIEKVITSENAHKIKAKIIAEAANGPTTPAADKILIDRNILVIPDLYIN
AGGVTVSFFEWLKNLNHVSYGRLTFKYERESNYHLLASIEESLDKALNDKSVQESLERRF
GRVGGKIPVTPSEAFQKRISGASEKDIVHSGLDYTMERSARAIMRTATRFNLGLDLRTAA
YVNSIEKIFTTYRDAGLAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g3564.t1 | CDD | cd01076 | NAD_bind_1_Glu_DH | 251 | 549 | 1.92868E-115 |
| 14 | g3564.t1 | Gene3D | G3DSA:1.10.287.140 | - | 51 | 101 | 7.4E-24 |
| 15 | g3564.t1 | Gene3D | G3DSA:3.40.50.10860 | Leucine Dehydrogenase | 102 | 250 | 1.1E-65 |
| 13 | g3564.t1 | Gene3D | G3DSA:3.40.50.720 | - | 251 | 559 | 6.1E-109 |
| 3 | g3564.t1 | PANTHER | PTHR11606 | GLUTAMATE DEHYDROGENASE | 49 | 467 | 8.2E-257 |
| 5 | g3564.t1 | PANTHER | PTHR11606:SF33 | GLUTAMATE DEHYDROGENASE 1 | 49 | 467 | 8.2E-257 |
| 4 | g3564.t1 | PANTHER | PTHR11606 | GLUTAMATE DEHYDROGENASE | 471 | 559 | 8.2E-257 |
| 6 | g3564.t1 | PANTHER | PTHR11606:SF33 | GLUTAMATE DEHYDROGENASE 1 | 471 | 559 | 8.2E-257 |
| 10 | g3564.t1 | PRINTS | PR00082 | Glutamate/leucine/phenylalanine/valine dehydrogenase signature | 157 | 171 | 3.1E-32 |
| 9 | g3564.t1 | PRINTS | PR00082 | Glutamate/leucine/phenylalanine/valine dehydrogenase signature | 242 | 264 | 3.1E-32 |
| 7 | g3564.t1 | PRINTS | PR00082 | Glutamate/leucine/phenylalanine/valine dehydrogenase signature | 292 | 312 | 3.1E-32 |
| 8 | g3564.t1 | PRINTS | PR00082 | Glutamate/leucine/phenylalanine/valine dehydrogenase signature | 419 | 430 | 3.1E-32 |
| 1 | g3564.t1 | Pfam | PF02812 | Glu/Leu/Phe/Val dehydrogenase, dimerisation domain | 102 | 229 | 3.5E-57 |
| 2 | g3564.t1 | Pfam | PF00208 | Glutamate/Leucine/Phenylalanine/Valine dehydrogenase | 251 | 444 | 1.9E-49 |
| 17 | g3564.t1 | ProSitePatterns | PS00074 | Glu / Leu / Phe / Val dehydrogenases active site. | 165 | 178 | - |
| 18 | g3564.t1 | SMART | SM00839 | ELFV_dehydrog_3 | 253 | 556 | 2.4E-88 |
| 12 | g3564.t1 | SUPERFAMILY | SSF53223 | Aminoacid dehydrogenase-like, N-terminal domain | 48 | 253 | 2.33E-67 |
| 11 | g3564.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 254 | 557 | 3.09E-81 |
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:0006520 | cellular amino acid metabolic process | BP |
| GO:0055114 | NA | NA |
| GO:0016639 | oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor | MF |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00261 (glutamate dehydrogenase (NAD(P)+))
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.
