Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative DNA-binding protein P3A2.

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 g3900 g3900.t5 TTS g3900.t5 28718078 28718078
chr_3 g3900 g3900.t5 isoform g3900.t5 28718171 28720063
chr_3 g3900 g3900.t5 exon g3900.t5.exon1 28718171 28718174
chr_3 g3900 g3900.t5 cds g3900.t5.CDS1 28718173 28718174
chr_3 g3900 g3900.t5 exon g3900.t5.exon2 28718240 28718552
chr_3 g3900 g3900.t5 cds g3900.t5.CDS2 28718240 28718552
chr_3 g3900 g3900.t5 exon g3900.t5.exon3 28718614 28719029
chr_3 g3900 g3900.t5 cds g3900.t5.CDS3 28718614 28718874
chr_3 g3900 g3900.t5 exon g3900.t5.exon4 28719985 28720063
chr_3 g3900 g3900.t5 TSS g3900.t5 28720067 28720067

Sequences

>g3900.t5 Gene=g3900 Length=812
TCGCGATTAAAAAGATTATTGATTTTTTCAAATTGGGCTGCAAAAGAAAATTTTTAATGG
GTGAAAAATTGAGGAAATAGTCACTACCGTTTTACAAAAAAAACTCTCAGACTCATTAAG
AAGAAAATATTAGCATATACACATATTCAGCAGCAATAGCGGCATCATTTTTTCAAATAG
AGTTGATAATAGCAAACAGATATGAATACCATAGCAACGACAGAGACTATAGAGATGGTT
GATGAAGGAGGACTTACTGATGATTCAGAGTCTGATTTTGATAGTCGACCAAGCAGCCCA
GACGAGGGAGATGGTAATTTACTAACTGAAGCTATGGAAAATGAAGTCACAGCACAACTT
GTCAATGCTGGTGTCGTTGGAATAGCTGCTGCAGCTGCCATTACATCTTCAAAGAAAAGA
AAACGTCCTCACTCGTTTGAAACAAATCCTTCCATCAGAAAACGACAACAAAATCGACTG
CTAAGGAAATTGAGGCAAACAATATTTGAGTATGCAACACGAGTTGGTCAGCAAGCAGTC
GTATTAGTTGCAACACCTGGTAAACCGAACAATATTTACAAAGTTTTTGGCGCGAAACCT
CTCGAAGATGTTATTAAAAATTTGCGCACGATGGTAATGGACGAACTCGAAACGGCATTA
GCTCAACAAGCACCACCAAAAGTACAGGAAGATCCATCACTGTTCGAATTGCCCCCTCTG
ATTATTGATGGGATTCCTACACCAGTCGAGAAGATGACACAAGCTCAATTGAGAGCATTT
ATTCCACTTATGCTTAAATATTCAACAGGACG

>g3900.t5 Gene=g3900 Length=192
MVDEGGLTDDSESDFDSRPSSPDEGDGNLLTEAMENEVTAQLVNAGVVGIAAAAAITSSK
KRKRPHSFETNPSIRKRQQNRLLRKLRQTIFEYATRVGQQAVVLVATPGKPNNIYKVFGA
KPLEDVIKNLRTMVMDELETALAQQAPPKVQEDPSLFELPPLIIDGIPTPVEKMTQAQLR
AFIPLMLKYSTG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
4 g3900.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 29 -
2 g3900.t5 PANTHER PTHR20338 NUCLEAR RESPIRATORY FACTOR 1 14 192 4.5E-93
3 g3900.t5 PANTHER PTHR20338:SF8 NUCLEAR RESPIRATORY FACTOR 1 14 192 4.5E-93
1 g3900.t5 Pfam PF10491 NLS-binding and DNA-binding and dimerisation domains of Nrf1 46 192 1.9E-73
6 g3900.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 37 -
7 g3900.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 38 57 -
5 g3900.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 58 192 -

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:0006357 regulation of transcription by RNA polymerase II BP
GO:0003700 DNA-binding transcription factor activity 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