Gene loci information

Transcript annotation

  • This transcript has been annotated as NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, 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_1 g13993 g13993.t3 TSS g13993.t3 33863845 33863845
chr_1 g13993 g13993.t3 isoform g13993.t3 33863924 33865548
chr_1 g13993 g13993.t3 exon g13993.t3.exon1 33863924 33864021
chr_1 g13993 g13993.t3 exon g13993.t3.exon2 33864126 33864455
chr_1 g13993 g13993.t3 exon g13993.t3.exon3 33864515 33864625
chr_1 g13993 g13993.t3 exon g13993.t3.exon4 33864727 33865548
chr_1 g13993 g13993.t3 cds g13993.t3.CDS1 33864784 33865548
chr_1 g13993 g13993.t3 TTS g13993.t3 33865643 33865643

Sequences

>g13993.t3 Gene=g13993 Length=1361
ATGGCTTATTCAATCTTAAGTAACATTGCTCGTAAAACGGCTGGTGCGAATCTATCGAAA
TCAGTGCTTCAGAACGTCGGTGCTCTTTATAATGCCAATCAAACAAGAGGCGGTGCAAAA
TGGTATCCGGATTCAGAGTTTGTACAACAATTCAGTGGCGCTGTAATGTATCCCGATGAA
GTTACTTCGAAATGGAAAGTTCCACCATATAACGCAAAAATGGCACCTCTTCCAGAAAAA
AATGTACGAAACATGAGTGTCAACTTTGGACCACAACATCCTGCTGCTCACGGTGTCTTA
CGTATGGTTTTAGAATTAGACGGTGAAACTGTTGTTCGTGCAGATCCTCATATTGGTCTT
TTGCATCGTGGCACTGAAAAATTGATTGAATATAAGACATATACTCAAGCCTTACCTTAT
TTCGATCGTCTTGATTATGTCTCAATGATGTGCAATGAGCAATGTTACTCACTTGCTGTT
GAGAAGCTTCTAAATATCGATATTCCATTGCGTGCAAAATATATTAGAGGTAATTTAAAG
CTCTTGATATTGGCGCATTAACACCATTCTTCTGGCTTTTTGAAGAGCGTGAGAAGATGA
TGGAATTCTATGAACGTGTATCAGGTGCTCGTATGCACGCTGCTTATATTCGTCCAGGCG
GTGTGAGTCAAGATTTGCCTCTTGGTCTTCTTGACGACATTTACGAGTTTGCATCGAAAT
TTAGCGAACGATTAGATGAAACTGAAGATCTTTTGACAAATAATCGCTTATGGATCCAAA
GAACAGAAGATATTGGTGTTGTAACAGCTGAAGAAGCTCTTAATTATGGCTTCAGTGGTG
TTATGCTGCGAGGATCAGGAATCAAATGGGATCTGCGCAAAACTCAACCTTATGACGCCT
ATCATTTAGTAGAATTTGACGTTCCAATTGGCACAAAGGGAGATTGTTACGATCGTTATT
TGTGTCGTGTTGAAGAAATGCGTCAATCTCTTAGAATTATTGATCAATGCTTAAATCAAA
TGCCACCAGGTGAAATTAAGGTTGATGACGCCAAATTAACACCACCATCACGTCACGAAA
TGAAAACGTCAATGGAAGCCCTCATTCATCACTTTAAACTATTCACACAAGGATATCAAG
TTCCTCCTGGCTCAACTTACACAGCAATTGAAGCTCCCAAAGGAGAATTTGGTGTTTATT
TAGTAGCTGACGGTTCAAGCAGACCATATAGATGTAAAATCAAACCTCCAGGCTTCGCAC
ATTTAGCTGCTATTGACAAAATTGGCAAGAATCATATGCTTGCTGATATTGTAGCCATTA
TTGGAACACTTGATGTTGTCTTTGGTGAAATTGATCGATAA

>g13993.t3 Gene=g13993 Length=254
MMEFYERVSGARMHAAYIRPGGVSQDLPLGLLDDIYEFASKFSERLDETEDLLTNNRLWI
QRTEDIGVVTAEEALNYGFSGVMLRGSGIKWDLRKTQPYDAYHLVEFDVPIGTKGDCYDR
YLCRVEEMRQSLRIIDQCLNQMPPGEIKVDDAKLTPPSRHEMKTSMEALIHHFKLFTQGY
QVPPGSTYTAIEAPKGEFGVYLVADGSSRPYRCKIKPPGFAHLAAIDKIGKNHMLADIVA
IIGTLDVVFGEIDR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g13993.t3 Gene3D G3DSA:1.10.645.20 - 1 254 0
2 g13993.t3 PANTHER PTHR11993 NADH-UBIQUINONE OXIDOREDUCTASE 49 KDA SUBUNIT 1 254 0
1 g13993.t3 Pfam PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit 1 254 0
3 g13993.t3 SUPERFAMILY SSF56762 HydB/Nqo4-like 2 254 0

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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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