General information for g13993.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial.
Parent gene
- The parent gene g13993 is located on chr_1: 33864706..33865618 (+ 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_1 | g13993 | g13993.t4 | TSS | g13993.t4 | 33863845 | 33863845 |
| chr_1 | g13993 | g13993.t4 | isoform | g13993.t4 | 33863924 | 33865548 |
| chr_1 | g13993 | g13993.t4 | exon | g13993.t4.exon1 | 33863924 | 33864455 |
| chr_1 | g13993 | g13993.t4 | cds | g13993.t4.CDS1 | 33864193 | 33864455 |
| chr_1 | g13993 | g13993.t4 | exon | g13993.t4.exon2 | 33864515 | 33864615 |
| chr_1 | g13993 | g13993.t4 | cds | g13993.t4.CDS2 | 33864515 | 33864615 |
| chr_1 | g13993 | g13993.t4 | exon | g13993.t4.exon3 | 33864671 | 33865548 |
| chr_1 | g13993 | g13993.t4 | cds | g13993.t4.CDS3 | 33864671 | 33865548 |
| chr_1 | g13993 | g13993.t4 | TTS | g13993.t4 | 33865643 | 33865643 |
Sequences
>g13993.t4 Gene=g13993 Length=1511
ATGGCTTATTCAATCTTAAGTAACATTGCTCGTAAAACGGCTGGTGCGAATCTATCGAAA
TCAGTGCTTCAGAACGTCGGTGCTCTTTATAATGCCAAGTAAATTGATAATTTTCCTAAT
TTATTGTTGTTGTTGTAATTTTTTCATTGCATAATTTTTCAAATATTTTGATACAAATCT
CCATATTTTGTAATTATTACAGTCAAACAAGAGGCGGTGCAAAATGGTATCCGGATTCAG
AGTTTGTACAACAATTCAGTGGCGCTGTAATGTATCCCGATGAAGTTACTTCGAAATGGA
AAGTTCCACCATATAACGCAAAAATGGCACCTCTTCCAGAAAAAAATGTACGAAACATGA
GTGTCAACTTTGGACCACAACATCCTGCTGCTCACGGTGTCTTACGTATGGTTTTAGAAT
TAGACGGTGAAACTGTTGTTCGTGCAGATCCTCATATTGGTCTTTTGCATCGTGGCACTG
AAAAATTGATTGAATATAAGACATATACTCAAGCCTTACCTTATTTCGATCGTCTTGATT
ATGTCTCAATGATGTGCAATGAGCAATGTTACTCACTTGCTGTTGAGAAGCTTCTAAATA
TCGATATTCCATTGCGTGCAAAATATATTAGAGTTTTATTTGCTGAAATTACGAGAATTT
TAAATCACATCATGGCTGTTGGCACGCATGCTCTTGATATTGGCGCATTAACACCATTCT
TCTGGCTTTTTGAAGAGCGTGAGAAGATGATGGAATTCTATGAACGTGTATCAGGTGCTC
GTATGCACGCTGCTTATATTCGTCCAGGCGGTGTGAGTCAAGATTTGCCTCTTGGTCTTC
TTGACGACATTTACGAGTTTGCATCGAAATTTAGCGAACGATTAGATGAAACTGAAGATC
TTTTGACAAATAATCGCTTATGGATCCAAAGAACAGAAGATATTGGTGTTGTAACAGCTG
AAGAAGCTCTTAATTATGGCTTCAGTGGTGTTATGCTGCGAGGATCAGGAATCAAATGGG
ATCTGCGCAAAACTCAACCTTATGACGCCTATCATTTAGTAGAATTTGACGTTCCAATTG
GCACAAAGGGAGATTGTTACGATCGTTATTTGTGTCGTGTTGAAGAAATGCGTCAATCTC
TTAGAATTATTGATCAATGCTTAAATCAAATGCCACCAGGTGAAATTAAGGTTGATGACG
CCAAATTAACACCACCATCACGTCACGAAATGAAAACGTCAATGGAAGCCCTCATTCATC
ACTTTAAACTATTCACACAAGGATATCAAGTTCCTCCTGGCTCAACTTACACAGCAATTG
AAGCTCCCAAAGGAGAATTTGGTGTTTATTTAGTAGCTGACGGTTCAAGCAGACCATATA
GATGTAAAATCAAACCTCCAGGCTTCGCACATTTAGCTGCTATTGACAAAATTGGCAAGA
ATCATATGCTTGCTGATATTGTAGCCATTATTGGAACACTTGATGTTGTCTTTGGTGAAA
TTGATCGATAA
>g13993.t4 Gene=g13993 Length=413
MYPDEVTSKWKVPPYNAKMAPLPEKNVRNMSVNFGPQHPAAHGVLRMVLELDGETVVRAD
PHIGLLHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIDIPLRAKYI
RVLFAEITRILNHIMAVGTHALDIGALTPFFWLFEEREKMMEFYERVSGARMHAAYIRPG
GVSQDLPLGLLDDIYEFASKFSERLDETEDLLTNNRLWIQRTEDIGVVTAEEALNYGFSG
VMLRGSGIKWDLRKTQPYDAYHLVEFDVPIGTKGDCYDRYLCRVEEMRQSLRIIDQCLNQ
MPPGEIKVDDAKLTPPSRHEMKTSMEALIHHFKLFTQGYQVPPGSTYTAIEAPKGEFGVY
LVADGSSRPYRCKIKPPGFAHLAAIDKIGKNHMLADIVAIIGTLDVVFGEIDR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13993.t4 | Gene3D | G3DSA:1.10.645.20 | - | 27 | 413 | 3.6E-185 |
| 3 | g13993.t4 | Hamap | MF_01358 | NAD(P)H-quinone oxidoreductase subunit H, chloroplastic [ndhH]. | 22 | 413 | 49.536354 |
| 2 | g13993.t4 | PANTHER | PTHR11993 | NADH-UBIQUINONE OXIDOREDUCTASE 49 KDA SUBUNIT | 25 | 413 | 7.5E-197 |
| 1 | g13993.t4 | Pfam | PF00346 | Respiratory-chain NADH dehydrogenase, 49 Kd subunit | 143 | 413 | 1.9E-125 |
| 5 | g13993.t4 | ProSitePatterns | PS00535 | Respiratory chain NADH dehydrogenase 49 Kd subunit signature. | 66 | 77 | - |
| 4 | g13993.t4 | SUPERFAMILY | SSF56762 | HydB/Nqo4-like | 39 | 413 | 6.8E-142 |
| 7 | g13993.t4 | TIGRFAM | TIGR01962 | NuoD: NADH dehydrogenase (quinone), D subunit | 29 | 413 | 8.8E-186 |
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:0016651 | oxidoreductase activity, acting on NAD(P)H | MF |
| GO:0051287 | NAD binding | MF |
| GO:0048038 | quinone binding | MF |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K03935 (NADH dehydrogenase (ubiquinone) Fe-S protein 2)
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.
