Gene loci information

Transcript annotation

  • This transcript has been annotated as Glycerol-3-phosphate dehydrogenase, mitochondrial.

Parent gene

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.t1 isoform g3166.t1 23418563 23421508
chr_3 g3166 g3166.t1 exon g3166.t1.exon1 23418563 23418925
chr_3 g3166 g3166.t1 cds g3166.t1.CDS1 23418563 23418925
chr_3 g3166 g3166.t1 exon g3166.t1.exon2 23418979 23419091
chr_3 g3166 g3166.t1 cds g3166.t1.CDS2 23418979 23419091
chr_3 g3166 g3166.t1 exon g3166.t1.exon3 23419146 23420604
chr_3 g3166 g3166.t1 cds g3166.t1.CDS3 23419146 23420604
chr_3 g3166 g3166.t1 exon g3166.t1.exon4 23420661 23420762
chr_3 g3166 g3166.t1 cds g3166.t1.CDS4 23420661 23420762
chr_3 g3166 g3166.t1 exon g3166.t1.exon5 23420819 23420949
chr_3 g3166 g3166.t1 cds g3166.t1.CDS5 23420819 23420949
chr_3 g3166 g3166.t1 exon g3166.t1.exon6 23421472 23421508
chr_3 g3166 g3166.t1 cds g3166.t1.CDS6 23421472 23421508
chr_3 g3166 g3166.t1 TTS g3166.t1 23421829 23421829
chr_3 g3166 g3166.t1 TSS g3166.t1 NA NA

Sequences

>g3166.t1 Gene=g3166 Length=2205
ATGGCATTTCGAAAATTAAGTGTAACCGCACTTGGTACATTGATTGGTGGCGGATTTGCA
ACATATGCTTTACGTCAAAATGACGATATGGTTGCAAGAGTACAACTTGAAGAGAAAGTC
ATCAAACGTGCTAGAAAATTACCACCAAGATCTGAACAAATCACATCATTACAATCAGGA
GAAGAATATGACGTTCTTATCATTGGTGGTGGTGCAACTGGTGCTGGTTGTGCTTTAGAT
GCTTGCACACGTGGATTAAAAACTGCCTTGGTTGAAGCCAATGACTTTGCGAGCGGAACC
TCGTCGAGATCGACAAAATTAATTCATGGTGGTGTTCGATATCTTCAAAAGGCTATCTTA
GGGCTTGATATCGAACAATACAATATGGTAAAAGAAGCCCTTCGTGAACGAGCTTCAATG
CTTCAATCTGCTCCTCATTTAACTCATCCATTGCCAATTATGTTGCCAGTTTATACATGG
TGGCAAGTGCCATATTTCTGGGTTGGTATTAAAGCTTATGACTTTGTTGCTGGCGATAGA
AATGTCAAATCAAGCTACTACTTATCAAAAGAGGATGCTCTTGAGAAATTTCCTATGTTA
AAGAGTGACAAACTTTGTGGTGCTATTGTGTACTATGATGGTCAACAAGATGATGCTCGT
ATGTGCATTTCAGTTGCTTTGACAGCTGCTCGTTATGGTGCAACAGTTGCAAATCATGTT
GAAGTCAAGGAATTGTTAAAAAAGAAAGATGAAAGTGGAAAGGAAGTTCTTTGTGGTGCA
AGAGTTGTTGATAATTTGACAAAGAAAGAGTGGACAATTAAAGCAAAATGTGTTATCAAT
GCAGCTGGTCCATTCACAGATAGCATTCGTAAAATGGATGATGCAAAAGTCAAAACAATT
TGTTGCCCAAGTTCAGGTGTTCACATCGTTTTACCTGGATACTATTCACCACAAGGTCTT
GGTTTACTTGATCCCGCAACAAGCGATGGTCGTGTAATTTTCTTCCTTCCATGGCTTCGT
GGAACAATTGCTGGCACAACAGATTCACCATGTGAGGTCACACGCAAGCCAGCACCAACT
GAAGATGACATTCAATTTATTTTGAGTGAAATTAAAAATTACCTTAACAAAGATGTTGAT
GTCCGTCGTGGTGATGTATTGAGTGCATGGTGTGGTATTCGTCCATTAGTGTCAGACCCA
AATAAAGACGATACTCAATCACTTGCTCGTAATCACATTGTGCATGTCAGTGATTCAAAA
CTTGTAACAATTGCTGGTGGCAAATGGACAACTTATCGTGCTATGGCTGAACATACACTC
GATGCTGCTATTAAAGCTTGCGACCTTAAACCACAACGTCCATGTATCACTGATAAAATT
CAAATTGAAGGCAGTCATGGTTGGACACCAACAATGTATATCAGATTGGTACAAGATTTT
GGTCTTGAAACTGAAGTCGCACAACATTTAGCTCAAGCTTATGGCGATCGTGCTTATCCT
GTTGCTAAATTAGCAGCTCTCACTGGCAAACGTTGGCCAATCATTGGCAAGCGTATTCAT
CCTGAATTCCCATATATTGATGGTGAAATTCGTTATGGTGTTCGCGAATATGCTTGCTCT
GCCATTGATATGGTAGCTAGACGTTTGAGATTAGCTTTCCTTAATGTTCAAGCTGCACAA
GAAGCTTTACCAACAATTGTTGATATCATGGCTGAAGAATTAAAATGGTCAAAGGAAGAA
AAAGAGAAACAAATTAAGGAGGCTACAGAATTCTTGAACCTTGAAATGGGTGCTGCTGTC
AATAAATCATTGAAAGACAAAGTACCAACTAACTTGGCTCCAGAAGAAGTTCAGAAATAC
AAGAAACGATTCGAAGTTATTGATAAGGAAAAGAAGGGCTATGTTTCAATTAATGATATT
CGTAGAGCTTTGAAGAGCTTTGGAGATGCTGATATTTCAGGAGAAGAACTTCATGAAATT
CTTCGTGAAATCGATACTAACATGAATGGACAAGTTGAACTTGAAGAATATCTTCAGATG
ATGGCTGCTATTAAATCTGGCACAGTCGCATATTCAAGATTTGCTCGTATCGCTGAGTCA
GAAGAAGCAAAACAAAATGAACTGAAAGCAAGAAACAAAATTTCAATTGAACGCTCAGGC
GGTGGTTTGAACTTAGACACTACGACTGATGGAAAGGAATCTTAA

>g3166.t1 Gene=g3166 Length=734
MAFRKLSVTALGTLIGGGFATYALRQNDDMVARVQLEEKVIKRARKLPPRSEQITSLQSG
EEYDVLIIGGGATGAGCALDACTRGLKTALVEANDFASGTSSRSTKLIHGGVRYLQKAIL
GLDIEQYNMVKEALRERASMLQSAPHLTHPLPIMLPVYTWWQVPYFWVGIKAYDFVAGDR
NVKSSYYLSKEDALEKFPMLKSDKLCGAIVYYDGQQDDARMCISVALTAARYGATVANHV
EVKELLKKKDESGKEVLCGARVVDNLTKKEWTIKAKCVINAAGPFTDSIRKMDDAKVKTI
CCPSSGVHIVLPGYYSPQGLGLLDPATSDGRVIFFLPWLRGTIAGTTDSPCEVTRKPAPT
EDDIQFILSEIKNYLNKDVDVRRGDVLSAWCGIRPLVSDPNKDDTQSLARNHIVHVSDSK
LVTIAGGKWTTYRAMAEHTLDAAIKACDLKPQRPCITDKIQIEGSHGWTPTMYIRLVQDF
GLETEVAQHLAQAYGDRAYPVAKLAALTGKRWPIIGKRIHPEFPYIDGEIRYGVREYACS
AIDMVARRLRLAFLNVQAAQEALPTIVDIMAEELKWSKEEKEKQIKEATEFLNLEMGAAV
NKSLKDKVPTNLAPEEVQKYKKRFEVIDKEKKGYVSINDIRRALKSFGDADISGEELHEI
LREIDTNMNGQVELEEYLQMMAAIKSGTVAYSRFARIAESEEAKQNELKARNKISIERSG
GGLNLDTTTDGKES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
26 g3166.t1 CDD cd00051 EFh 619 682 1.76237E-13
20 g3166.t1 Coils Coil Coil 124 144 -
19 g3166.t1 Coils Coil Coil 571 591 -
16 g3166.t1 Gene3D G3DSA:3.50.50.60 - 64 440 4.9E-138
18 g3166.t1 Gene3D G3DSA:3.30.9.10 - 148 397 4.9E-138
15 g3166.t1 Gene3D G3DSA:1.10.8.870 - 470 603 3.3E-38
17 g3166.t1 Gene3D G3DSA:1.10.238.10 - 604 716 6.3E-17
4 g3166.t1 PANTHER PTHR11985 GLYCEROL-3-PHOSPHATE DEHYDROGENASE 10 665 3.8E-279
5 g3166.t1 PANTHER PTHR11985:SF29 GLYCEROL-3-PHOSPHATE DEHYDROGENASE, MITOCHONDRIAL 10 665 3.8E-279
7 g3166.t1 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature 63 75 8.1E-35
9 g3166.t1 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature 76 86 8.1E-35
11 g3166.t1 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature 92 104 8.1E-35
8 g3166.t1 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature 144 156 8.1E-35
10 g3166.t1 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature 390 396 8.1E-35
6 g3166.t1 PRINTS PR01001 FAD-dependent glycerol-3-phosphate dehydrogenase family signature 421 433 8.1E-35
2 g3166.t1 Pfam PF01266 FAD dependent oxidoreductase 64 432 2.9E-53
3 g3166.t1 Pfam PF16901 C-terminal domain of alpha-glycerophosphate oxidase 455 581 6.2E-40
1 g3166.t1 Pfam PF13499 EF-hand domain pair 619 681 2.7E-10
22 g3166.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 25 -
23 g3166.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
24 g3166.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
25 g3166.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 25 -
21 g3166.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 26 734 -
29 g3166.t1 ProSitePatterns PS00977 FAD-dependent glycerol-3-phosphate dehydrogenase signature 1. 68 85 -
31 g3166.t1 ProSitePatterns PS00978 FAD-dependent glycerol-3-phosphate dehydrogenase signature 2. 426 436 -
30 g3166.t1 ProSitePatterns PS00018 EF-hand calcium-binding domain. 665 677 -
33 g3166.t1 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 615 650 12.198
32 g3166.t1 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 652 687 12.114
27 g3166.t1 SMART SM00054 efh_1 619 647 1.9
28 g3166.t1 SMART SM00054 efh_1 656 684 1.4E-4
14 g3166.t1 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain 50 304 2.33E-43
13 g3166.t1 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain 303 396 1.61E-5
12 g3166.t1 SUPERFAMILY SSF47473 EF-hand 607 681 2.09E-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

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.

Raw TPM values