Gene loci information

Transcript annotation

  • This transcript has been annotated as 60S ribosomal export protein NMD3.

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_2 g8094 g8094.t3 TSS g8094.t3 28551279 28551279
chr_2 g8094 g8094.t3 isoform g8094.t3 28551508 28553029
chr_2 g8094 g8094.t3 exon g8094.t3.exon1 28551508 28552773
chr_2 g8094 g8094.t3 cds g8094.t3.CDS1 28551878 28552773
chr_2 g8094 g8094.t3 exon g8094.t3.exon2 28552834 28553029
chr_2 g8094 g8094.t3 cds g8094.t3.CDS2 28552834 28553029
chr_2 g8094 g8094.t3 TTS g8094.t3 28553112 28553112

Sequences

>g8094.t3 Gene=g8094 Length=1462
ATTGTGTTGTGGTTGTGGATCATTGATTGATCCAAATCCATTAAATCAATGTGCAGCATG
TTTACGAACTCACATTGATATAACAGAGAACATTCCTAAACAAGGAACTCTCTTCTTTTG
CCGTAACTGTGAAAGATATTTGAATCCACCAAGTGAGTGGGTACATGCATCTCTGGAATC
GCGTGAATTGCTCTCAATTTGTCTTAAAAGAATCAAAGGATTAAAAGATGTGAAACTTAT
TGATGCAGGATTTATTTGGACAGAGCCCCATTCAAAGAGAATCAAAGTTAAACTCACTGT
TCATGCTGAAGTGTCTAATGGCATCGTATTGCAACAAGTTTTTGTGGTTGAGTTCACTGT
AACTAATCAAATGTGTGATGATTGTCATCGTCATGAAGCAAAAGATTACTGGAAATGTAT
GGTTCAAGTAAGACAAAAGGCTTCTAACAAAAAGACACTTTATTATATGGAACAAATGAT
TCTGAAGCATAAAGCTCACGAAAACTCTTTAGGAATTAAAAACAATTCAAGTGGATTAGA
CTTCTTTTATTCTGGTGAAAACCATGCTCGTAAAATGGTAGATTTTCTACAGACAATTCT
TCCAGTGAAAATGACTCAATCAAAAAAGCTCATTAGTCATGATATTCATAGCAACATTTA
CAACTATAAATTTACATGGGCATTAGATATTGTACCAATATCTAAAGGCAGTTTAGTTTG
TATTGGCAAGAAATTACAGCAAAACTATGGAAATATTGCACCTATTTGCCTCGTACAGAA
TGTTGCTAATGTGATACATGTCATAGATCCTCTAACTGCACAAATTGCTGAAATATCAGG
ATCAAATTATTTTAGATATCCTTTCACATCGATTTCGGATCCGAAGCAACTTATTGAATA
TACTGTTATGGATATAGAAATTATAAAAGATCGAAAACAATTTCCTGGACAAGGACCAAT
ATCTTTTAAACATGTTGTCGCTGATGTTTGGTTAGTAAAATCATCTGAACTTGGTATCAA
TGAATCAAATATTCACACAAAAACACACTTGGGACATTTGTTAAAGCCAGGTGATTCAGT
TATGGGTTATGATTTACGTGATGCTGTAATTAATAATGCTGATTTTGAAAAGTTGAAGAA
TGAAAATATTCCTGATGTCGTAATCGTTAAAAAGAATTACGGTGATAAGGATAAGAGACG
TCGTATGAGAAAATGGAAATTGAAACATCTCACAGAAGACGTTGGAAGCAGCTCAGATAT
TGGAAACGATTATAATGAATTTCTTGAAGACTTGGAAGAGGATGAAGAAATGCGTCAAAA
GGTTAATATTTATAAAGATAGCAGGAAGCAGCAAATTCCTGTTGATGTAAATGATATGGA
GGACCCATCTTGTCCACAAATTACACTTGAAGAAATGCTTGATGATCTTGTTATCGATGA
TGTTGATATGGGCAATGCATAA

>g8094.t3 Gene=g8094 Length=363
MCDDCHRHEAKDYWKCMVQVRQKASNKKTLYYMEQMILKHKAHENSLGIKNNSSGLDFFY
SGENHARKMVDFLQTILPVKMTQSKKLISHDIHSNIYNYKFTWALDIVPISKGSLVCIGK
KLQQNYGNIAPICLVQNVANVIHVIDPLTAQIAEISGSNYFRYPFTSISDPKQLIEYTVM
DIEIIKDRKQFPGQGPISFKHVVADVWLVKSSELGINESNIHTKTHLGHLLKPGDSVMGY
DLRDAVINNADFEKLKNENIPDVVIVKKNYGDKDKRRRMRKWKLKHLTEDVGSSSDIGND
YNEFLEDLEEDEEMRQKVNIYKDSRKQQIPVDVNDMEDPSCPQITLEEMLDDLVIDDVDM
GNA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g8094.t3 PANTHER PTHR12746:SF2 60S RIBOSOMAL EXPORT PROTEIN NMD3 1 354 0
3 g8094.t3 PANTHER PTHR12746 NONSENSE-MEDIATED MRNA DECAY PROTEIN 3 1 354 0
1 g8094.t3 Pfam PF04981 NMD3 family 1 107 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:0043023 ribosomal large subunit binding MF

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.

Raw TPM values