General information for g13993.t6
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.t6 | TSS | g13993.t6 | 33863845 | 33863845 |
| chr_1 | g13993 | g13993.t6 | isoform | g13993.t6 | 33863924 | 33865618 |
| chr_1 | g13993 | g13993.t6 | exon | g13993.t6.exon1 | 33863924 | 33864021 |
| chr_1 | g13993 | g13993.t6 | cds | g13993.t6.CDS1 | 33863924 | 33864021 |
| chr_1 | g13993 | g13993.t6 | exon | g13993.t6.exon2 | 33864126 | 33864455 |
| chr_1 | g13993 | g13993.t6 | cds | g13993.t6.CDS2 | 33864126 | 33864455 |
| chr_1 | g13993 | g13993.t6 | exon | g13993.t6.exon3 | 33864515 | 33864615 |
| chr_1 | g13993 | g13993.t6 | cds | g13993.t6.CDS3 | 33864515 | 33864615 |
| chr_1 | g13993 | g13993.t6 | exon | g13993.t6.exon4 | 33864671 | 33865531 |
| chr_1 | g13993 | g13993.t6 | cds | g13993.t6.CDS4 | 33864671 | 33865531 |
| chr_1 | g13993 | g13993.t6 | exon | g13993.t6.exon5 | 33865591 | 33865618 |
| chr_1 | g13993 | g13993.t6 | cds | g13993.t6.CDS5 | 33865591 | 33865601 |
| chr_1 | g13993 | g13993.t6 | TTS | g13993.t6 | 33865643 | 33865643 |
Sequences
>g13993.t6 Gene=g13993 Length=1418
ATGGCTTATTCAATCTTAAGTAACATTGCTCGTAAAACGGCTGGTGCGAATCTATCGAAA
TCAGTGCTTCAGAACGTCGGTGCTCTTTATAATGCCAATCAAACAAGAGGCGGTGCAAAA
TGGTATCCGGATTCAGAGTTTGTACAACAATTCAGTGGCGCTGTAATGTATCCCGATGAA
GTTACTTCGAAATGGAAAGTTCCACCATATAACGCAAAAATGGCACCTCTTCCAGAAAAA
AATGTACGAAACATGAGTGTCAACTTTGGACCACAACATCCTGCTGCTCACGGTGTCTTA
CGTATGGTTTTAGAATTAGACGGTGAAACTGTTGTTCGTGCAGATCCTCATATTGGTCTT
TTGCATCGTGGCACTGAAAAATTGATTGAATATAAGACATATACTCAAGCCTTACCTTAT
TTCGATCGTCTTGATTATGTCTCAATGATGTGCAATGAGCAATGTTACTCACTTGCTGTT
GAGAAGCTTCTAAATATCGATATTCCATTGCGTGCAAAATATATTAGAGTTTTATTTGCT
GAAATTACGAGAATTTTAAATCACATCATGGCTGTTGGCACGCATGCTCTTGATATTGGC
GCATTAACACCATTCTTCTGGCTTTTTGAAGAGCGTGAGAAGATGATGGAATTCTATGAA
CGTGTATCAGGTGCTCGTATGCACGCTGCTTATATTCGTCCAGGCGGTGTGAGTCAAGAT
TTGCCTCTTGGTCTTCTTGACGACATTTACGAGTTTGCATCGAAATTTAGCGAACGATTA
GATGAAACTGAAGATCTTTTGACAAATAATCGCTTATGGATCCAAAGAACAGAAGATATT
GGTGTTGTAACAGCTGAAGAAGCTCTTAATTATGGCTTCAGTGGTGTTATGCTGCGAGGA
TCAGGAATCAAATGGGATCTGCGCAAAACTCAACCTTATGACGCCTATCATTTAGTAGAA
TTTGACGTTCCAATTGGCACAAAGGGAGATTGTTACGATCGTTATTTGTGTCGTGTTGAA
GAAATGCGTCAATCTCTTAGAATTATTGATCAATGCTTAAATCAAATGCCACCAGGTGAA
ATTAAGGTTGATGACGCCAAATTAACACCACCATCACGTCACGAAATGAAAACGTCAATG
GAAGCCCTCATTCATCACTTTAAACTATTCACACAAGGATATCAAGTTCCTCCTGGCTCA
ACTTACACAGCAATTGAAGCTCCCAAAGGAGAATTTGGTGTTTATTTAGTAGCTGACGGT
TCAAGCAGACCATATAGATGTAAAATCAAACCTCCAGGCTTCGCACATTTAGCTGCTATT
GACAAAATTGGCAAGAATCATATGCTTGCTGATATTGTAGCCATTATTGGAACACTTGAT
GTTGTCTTTGAAAAAATATAACAAAATTGGAATGTTCA
>g13993.t6 Gene=g13993 Length=466
MAYSILSNIARKTAGANLSKSVLQNVGALYNANQTRGGAKWYPDSEFVQQFSGAVMYPDE
VTSKWKVPPYNAKMAPLPEKNVRNMSVNFGPQHPAAHGVLRMVLELDGETVVRADPHIGL
LHRGTEKLIEYKTYTQALPYFDRLDYVSMMCNEQCYSLAVEKLLNIDIPLRAKYIRVLFA
EITRILNHIMAVGTHALDIGALTPFFWLFEEREKMMEFYERVSGARMHAAYIRPGGVSQD
LPLGLLDDIYEFASKFSERLDETEDLLTNNRLWIQRTEDIGVVTAEEALNYGFSGVMLRG
SGIKWDLRKTQPYDAYHLVEFDVPIGTKGDCYDRYLCRVEEMRQSLRIIDQCLNQMPPGE
IKVDDAKLTPPSRHEMKTSMEALIHHFKLFTQGYQVPPGSTYTAIEAPKGEFGVYLVADG
SSRPYRCKIKPPGFAHLAAIDKIGKNHMLADIVAIIGTLDVVFEKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g13993.t6 | Gene3D | G3DSA:1.10.645.20 | - | 82 | 466 | 6.8E-182 |
| 3 | g13993.t6 | Hamap | MF_01358 | NAD(P)H-quinone oxidoreductase subunit H, chloroplastic [ndhH]. | 77 | 465 | 47.667038 |
| 2 | g13993.t6 | PANTHER | PTHR11993 | NADH-UBIQUINONE OXIDOREDUCTASE 49 KDA SUBUNIT | 80 | 465 | 1.2E-194 |
| 1 | g13993.t6 | Pfam | PF00346 | Respiratory-chain NADH dehydrogenase, 49 Kd subunit | 198 | 464 | 4.3E-122 |
| 5 | g13993.t6 | ProSitePatterns | PS00535 | Respiratory chain NADH dehydrogenase 49 Kd subunit signature. | 121 | 132 | - |
| 4 | g13993.t6 | SUPERFAMILY | SSF56762 | HydB/Nqo4-like | 94 | 463 | 1.44E-139 |
| 7 | g13993.t6 | TIGRFAM | TIGR01962 | NuoD: NADH dehydrogenase (quinone), D subunit | 84 | 465 | 9.4E-183 |
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. There were no conditions that were differentially expressed