Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Protein shuttle craft.

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 g4469 g4469.t5 TSS g4469.t5 2730368 2730368
chr_2 g4469 g4469.t5 isoform g4469.t5 2730400 2731713
chr_2 g4469 g4469.t5 exon g4469.t5.exon1 2730400 2730473
chr_2 g4469 g4469.t5 exon g4469.t5.exon2 2730610 2731713
chr_2 g4469 g4469.t5 cds g4469.t5.CDS1 2730650 2731711
chr_2 g4469 g4469.t5 TTS g4469.t5 NA NA

Sequences

>g4469.t5 Gene=g4469 Length=1178
GGTAATTATTTTAATAATAAAATTCAAGTGTAAATTAAGGCTTGAATTAAATTAATATTA
TATTGGTCAAGTAGATCACACATTTCTTCATAAATTCGTAGAAAGTGTAAAAGAATGTCG
CCTGTATCAGGAGAAGAAAGTAGTGCAACTCAGTCAAATTTAAATGCCAACGCATCAGAA
TTTATTCCGATTATGATTAATGAAGAATCGACTCAATTAGCAACAACAAATTCAATTCAT
TCAACTACTGGTGCTATTCCCAAAAAATTTTATAAAAGTAACAATAATTATCGTCGTGAT
AAGTTTGATAGAAATCAAAGATGGAGATCTAATAATGGTAGTAGTAGTCAACGAAGAGAG
ACTTTTGCAGAACGTAATAATAGAAATGAAAATGCTAATTTCGAACCATTAGAAAGTAAT
AACCAAAATAAAAAGTTCTTTGCTAATAATAAACCACCGAAACAAAATGATAGAATGAAT
GATCAAAATCAGTATGAAGGATCATCTCAAACAATTCAAAGACAAAATATTTCACGACAG
ATTAAAAATGCACAAATGTCAAATAATAATAGATTGAAAAATAATAATCGATATGGAGAA
AATGAAGTGCTTAGTGAAAGACAATATTACAATCGTCGTAACAATAATTATGGTCGAAAT
TATAATGGAATTCGATCTAATAATGAAAATCAGAAGAAAGAAGTTGAACAAAATCAACAA
GAAGAAGTTAATGAAAAGCCAACTACAAAAAATCGTCCAAAAAAACGTGAACCGTTTAAT
CGTAAAAAGGATGAATCAAAAGCTTCAAGTGCTTCACAACGTGATCGATTGATAAAAGAA
ATTGAATCAAATACATTAGAGTGCATGATATGTTGTGAAAAGATTAAGTCTTATCAACCA
ATTTGGAGTTGCTCAAACTGTTATCACATTCTTCACTTATATTGTATCAAAACTTGGATG
AAAAATTCAAAAAATGATGAAGGTGAATGGAGATGCCCAGCATGTAATCAAATGACAAAT
CAAAAGCCTGGTGATTATTTATGTTTTTGTGGTAAACTTAAAAATCCAGCTGTAAATCGC
AATGATCTAGCTCATTCATGTGGTGAAATGTGTATGAATCAAACACTTTGTCCACATCCT
TGTCAATTAAAATGTCATCCAGGTCCGCATGAAATTTG

>g4469.t5 Gene=g4469 Length=354
MSPVSGEESSATQSNLNANASEFIPIMINEESTQLATTNSIHSTTGAIPKKFYKSNNNYR
RDKFDRNQRWRSNNGSSSQRRETFAERNNRNENANFEPLESNNQNKKFFANNKPPKQNDR
MNDQNQYEGSSQTIQRQNISRQIKNAQMSNNNRLKNNNRYGENEVLSERQYYNRRNNNYG
RNYNGIRSNNENQKKEVEQNQQEEVNEKPTTKNRPKKREPFNRKKDESKASSASQRDRLI
KEIESNTLECMICCEKIKSYQPIWSCSNCYHILHLYCIKTWMKNSKNDEGEWRCPACNQM
TNQKPGDYLCFCGKLKNPAVNRNDLAHSCGEMCMNQTLCPHPCQLKCHPGPHEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g4469.t5 CDD cd16696 RING-CH-C4HC3_NFX1 249 298 1.41869E-20
5 g4469.t5 Coils Coil Coil 183 208 -
4 g4469.t5 Gene3D G3DSA:3.30.40.10 Zinc/RING finger domain 219 306 1.6E-9
9 g4469.t5 MobiDBLite mobidb-lite consensus disorder prediction 53 105 -
13 g4469.t5 MobiDBLite mobidb-lite consensus disorder prediction 55 69 -
8 g4469.t5 MobiDBLite mobidb-lite consensus disorder prediction 89 105 -
11 g4469.t5 MobiDBLite mobidb-lite consensus disorder prediction 146 238 -
12 g4469.t5 MobiDBLite mobidb-lite consensus disorder prediction 146 190 -
10 g4469.t5 MobiDBLite mobidb-lite consensus disorder prediction 191 238 -
1 g4469.t5 PANTHER PTHR12360:SF12 TRANSCRIPTIONAL REPRESSOR NF-X1 105 352 3.1E-45
2 g4469.t5 PANTHER PTHR12360 NUCLEAR TRANSCRIPTION FACTOR, X-BOX BINDING 1 NFX1 105 352 3.1E-45
7 g4469.t5 ProSitePatterns PS01359 Zinc finger PHD-type signature. 250 297 -
15 g4469.t5 ProSiteProfiles PS50016 Zinc finger PHD-type profile. 247 300 9.179
14 g4469.t5 ProSiteProfiles PS50089 Zinc finger RING-type profile. 250 298 11.014
3 g4469.t5 SUPERFAMILY SSF57850 RING/U-box 240 304 2.12E-12

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: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