General information for g3166.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glycerol-3-phosphate dehydrogenase, mitochondrial.
Parent gene
- The parent gene g3166 is located on chr_3: 23421471..23421834 (+ 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 | g3166 | g3166.t3 | isoform | g3166.t3 | 23418541 | 23420945 |
| chr_3 | g3166 | g3166.t3 | exon | g3166.t3.exon1 | 23418541 | 23418925 |
| chr_3 | g3166 | g3166.t3 | cds | g3166.t3.CDS1 | 23418563 | 23418925 |
| chr_3 | g3166 | g3166.t3 | exon | g3166.t3.exon2 | 23418979 | 23419091 |
| chr_3 | g3166 | g3166.t3 | cds | g3166.t3.CDS2 | 23418979 | 23419091 |
| chr_3 | g3166 | g3166.t3 | exon | g3166.t3.exon3 | 23419146 | 23420604 |
| chr_3 | g3166 | g3166.t3 | cds | g3166.t3.CDS3 | 23419146 | 23420604 |
| chr_3 | g3166 | g3166.t3 | exon | g3166.t3.exon4 | 23420661 | 23420762 |
| chr_3 | g3166 | g3166.t3 | cds | g3166.t3.CDS4 | 23420661 | 23420762 |
| chr_3 | g3166 | g3166.t3 | exon | g3166.t3.exon5 | 23420819 | 23420945 |
| chr_3 | g3166 | g3166.t3 | cds | g3166.t3.CDS5 | 23420819 | 23420944 |
| chr_3 | g3166 | g3166.t3 | TTS | g3166.t3 | 23421829 | 23421829 |
| chr_3 | g3166 | g3166.t3 | TSS | g3166.t3 | NA | NA |
Sequences
>g3166.t3 Gene=g3166 Length=2186
GTGAAGAAGACGAAAAAATAAAATGGCATTTCGAAAATTAAGTGTAACCGCACTTGGTAC
ATTGATTGGTGGCGGATTTGCAACATATGCTTTACGTCAAAATGACGATATGGTTGCAAG
AGTACAACTTGAAGAGAAAGTCATCAAACGTGCTAGAAAATTACCACCAAGATCTGAACA
AATCACATCATTACAATCAGGAGAAGAATATGACGTTCTTATCATTGGTGGTGGTGCAAC
TGGTGCTGGTTGTGCTTTAGATGCTTGCACACGTGGATTAAAAACTGCCTTGGTTGAAGC
CAATGACTTTGCGAGCGGAACCTCGTCGAGATCGACAAAATTAATTCATGGTGGTGTTCG
ATATCTTCAAAAGGCTATCTTAGGGCTTGATATCGAACAATACAATATGGTAAAAGAAGC
CCTTCGTGAACGAGCTTCAATGCTTCAATCTGCTCCTCATTTAACTCATCCATTGCCAAT
TATGTTGCCAGTTTATACATGGTGGCAAGTGCCATATTTCTGGGTTGGTATTAAAGCTTA
TGACTTTGTTGCTGGCGATAGAAATGTCAAATCAAGCTACTACTTATCAAAAGAGGATGC
TCTTGAGAAATTTCCTATGTTAAAGAGTGACAAACTTTGTGGTGCTATTGTGTACTATGA
TGGTCAACAAGATGATGCTCGTATGTGCATTTCAGTTGCTTTGACAGCTGCTCGTTATGG
TGCAACAGTTGCAAATCATGTTGAAGTCAAGGAATTGTTAAAAAAGAAAGATGAAAGTGG
AAAGGAAGTTCTTTGTGGTGCAAGAGTTGTTGATAATTTGACAAAGAAAGAGTGGACAAT
TAAAGCAAAATGTGTTATCAATGCAGCTGGTCCATTCACAGATAGCATTCGTAAAATGGA
TGATGCAAAAGTCAAAACAATTTGTTGCCCAAGTTCAGGTGTTCACATCGTTTTACCTGG
ATACTATTCACCACAAGGTCTTGGTTTACTTGATCCCGCAACAAGCGATGGTCGTGTAAT
TTTCTTCCTTCCATGGCTTCGTGGAACAATTGCTGGCACAACAGATTCACCATGTGAGGT
CACACGCAAGCCAGCACCAACTGAAGATGACATTCAATTTATTTTGAGTGAAATTAAAAA
TTACCTTAACAAAGATGTTGATGTCCGTCGTGGTGATGTATTGAGTGCATGGTGTGGTAT
TCGTCCATTAGTGTCAGACCCAAATAAAGACGATACTCAATCACTTGCTCGTAATCACAT
TGTGCATGTCAGTGATTCAAAACTTGTAACAATTGCTGGTGGCAAATGGACAACTTATCG
TGCTATGGCTGAACATACACTCGATGCTGCTATTAAAGCTTGCGACCTTAAACCACAACG
TCCATGTATCACTGATAAAATTCAAATTGAAGGCAGTCATGGTTGGACACCAACAATGTA
TATCAGATTGGTACAAGATTTTGGTCTTGAAACTGAAGTCGCACAACATTTAGCTCAAGC
TTATGGCGATCGTGCTTATCCTGTTGCTAAATTAGCAGCTCTCACTGGCAAACGTTGGCC
AATCATTGGCAAGCGTATTCATCCTGAATTCCCATATATTGATGGTGAAATTCGTTATGG
TGTTCGCGAATATGCTTGCTCTGCCATTGATATGGTAGCTAGACGTTTGAGATTAGCTTT
CCTTAATGTTCAAGCTGCACAAGAAGCTTTACCAACAATTGTTGATATCATGGCTGAAGA
ATTAAAATGGTCAAAGGAAGAAAAAGAGAAACAAATTAAGGAGGCTACAGAATTCTTGAA
CCTTGAAATGGGTGCTGCTGTCAATAAATCATTGAAAGACAAAGTACCAACTAACTTGGC
TCCAGAAGAAGTTCAGAAATACAAGAAACGATTCGAAGTTATTGATAAGGAAAAGAAGGG
CTATGTTTCAATTAATGATATTCGTAGAGCTTTGAAGAGCTTTGGAGATGCTGATATTTC
AGGAGAAGAACTTCATGAAATTCTTCGTGAAATCGATACTAACATGAATGGACAAGTTGA
ACTTGAAGAATATCTTCAGATGATGGCTGCTATTAAATCTGGCACAGTCGCATATTCAAG
ATTTGCTCGTATCGCTGAGTCAGAAGAAGCAAAACAAAATGAACTGAAAGCAAGAAACAA
AATTTCAATTGAACGCTCAGGCGGTG
>g3166.t3 Gene=g3166 Length=721
MAFRKLSVTALGTLIGGGFATYALRQNDDMVARVQLEEKVIKRARKLPPRSEQITSLQSG
EEYDVLIIGGGATGAGCALDACTRGLKTALVEANDFASGTSSRSTKLIHGGVRYLQKAIL
GLDIEQYNMVKEALRERASMLQSAPHLTHPLPIMLPVYTWWQVPYFWVGIKAYDFVAGDR
NVKSSYYLSKEDALEKFPMLKSDKLCGAIVYYDGQQDDARMCISVALTAARYGATVANHV
EVKELLKKKDESGKEVLCGARVVDNLTKKEWTIKAKCVINAAGPFTDSIRKMDDAKVKTI
CCPSSGVHIVLPGYYSPQGLGLLDPATSDGRVIFFLPWLRGTIAGTTDSPCEVTRKPAPT
EDDIQFILSEIKNYLNKDVDVRRGDVLSAWCGIRPLVSDPNKDDTQSLARNHIVHVSDSK
LVTIAGGKWTTYRAMAEHTLDAAIKACDLKPQRPCITDKIQIEGSHGWTPTMYIRLVQDF
GLETEVAQHLAQAYGDRAYPVAKLAALTGKRWPIIGKRIHPEFPYIDGEIRYGVREYACS
AIDMVARRLRLAFLNVQAAQEALPTIVDIMAEELKWSKEEKEKQIKEATEFLNLEMGAAV
NKSLKDKVPTNLAPEEVQKYKKRFEVIDKEKKGYVSINDIRRALKSFGDADISGEELHEI
LREIDTNMNGQVELEEYLQMMAAIKSGTVAYSRFARIAESEEAKQNELKARNKISIERSG
G
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 26 | g3166.t3 | CDD | cd00051 | EFh | 619 | 682 | 1.50942E-13 |
| 20 | g3166.t3 | Coils | Coil | Coil | 124 | 144 | - |
| 19 | g3166.t3 | Coils | Coil | Coil | 571 | 591 | - |
| 16 | g3166.t3 | Gene3D | G3DSA:3.50.50.60 | - | 64 | 440 | 4.7E-138 |
| 18 | g3166.t3 | Gene3D | G3DSA:3.30.9.10 | - | 148 | 397 | 4.7E-138 |
| 15 | g3166.t3 | Gene3D | G3DSA:1.10.8.870 | - | 470 | 603 | 3.2E-38 |
| 17 | g3166.t3 | Gene3D | G3DSA:1.10.238.10 | - | 604 | 716 | 6.0E-17 |
| 4 | g3166.t3 | PANTHER | PTHR11985 | GLYCEROL-3-PHOSPHATE DEHYDROGENASE | 10 | 665 | 3.6E-279 |
| 5 | g3166.t3 | PANTHER | PTHR11985:SF29 | GLYCEROL-3-PHOSPHATE DEHYDROGENASE, MITOCHONDRIAL | 10 | 665 | 3.6E-279 |
| 7 | g3166.t3 | PRINTS | PR01001 | FAD-dependent glycerol-3-phosphate dehydrogenase family signature | 63 | 75 | 7.4E-35 |
| 9 | g3166.t3 | PRINTS | PR01001 | FAD-dependent glycerol-3-phosphate dehydrogenase family signature | 76 | 86 | 7.4E-35 |
| 11 | g3166.t3 | PRINTS | PR01001 | FAD-dependent glycerol-3-phosphate dehydrogenase family signature | 92 | 104 | 7.4E-35 |
| 8 | g3166.t3 | PRINTS | PR01001 | FAD-dependent glycerol-3-phosphate dehydrogenase family signature | 144 | 156 | 7.4E-35 |
| 10 | g3166.t3 | PRINTS | PR01001 | FAD-dependent glycerol-3-phosphate dehydrogenase family signature | 390 | 396 | 7.4E-35 |
| 6 | g3166.t3 | PRINTS | PR01001 | FAD-dependent glycerol-3-phosphate dehydrogenase family signature | 421 | 433 | 7.4E-35 |
| 2 | g3166.t3 | Pfam | PF01266 | FAD dependent oxidoreductase | 64 | 432 | 2.8E-53 |
| 3 | g3166.t3 | Pfam | PF16901 | C-terminal domain of alpha-glycerophosphate oxidase | 455 | 581 | 6.0E-40 |
| 1 | g3166.t3 | Pfam | PF13499 | EF-hand domain pair | 619 | 681 | 2.7E-10 |
| 22 | g3166.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 23 | g3166.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 24 | g3166.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 17 | - |
| 25 | g3166.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 25 | - |
| 21 | g3166.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 721 | - |
| 29 | g3166.t3 | ProSitePatterns | PS00977 | FAD-dependent glycerol-3-phosphate dehydrogenase signature 1. | 68 | 85 | - |
| 31 | g3166.t3 | ProSitePatterns | PS00978 | FAD-dependent glycerol-3-phosphate dehydrogenase signature 2. | 426 | 436 | - |
| 30 | g3166.t3 | ProSitePatterns | PS00018 | EF-hand calcium-binding domain. | 665 | 677 | - |
| 33 | g3166.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 615 | 650 | 12.198 |
| 32 | g3166.t3 | ProSiteProfiles | PS50222 | EF-hand calcium-binding domain profile. | 652 | 687 | 12.114 |
| 27 | g3166.t3 | SMART | SM00054 | efh_1 | 619 | 647 | 1.9 |
| 28 | g3166.t3 | SMART | SM00054 | efh_1 | 656 | 684 | 1.4E-4 |
| 14 | g3166.t3 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain | 50 | 304 | 2.46E-43 |
| 13 | g3166.t3 | SUPERFAMILY | SSF54373 | FAD-linked reductases, C-terminal domain | 303 | 396 | 1.57E-5 |
| 12 | g3166.t3 | SUPERFAMILY | SSF47473 | EF-hand | 607 | 681 | 2.26E-16 |
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:0009331 | glycerol-3-phosphate dehydrogenase complex | CC |
| GO:0006072 | glycerol-3-phosphate metabolic process | BP |
| GO:0005509 | calcium ion binding | MF |
| GO:0055114 | NA | NA |
| GO:0004368 | glycerol-3-phosphate dehydrogenase (quinone) activity | MF |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00111 (glycerol-3-phosphate dehydrogenase)
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.
