General information for g4469.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Protein shuttle craft.
Parent gene
- The parent gene g4469 is located on chr_2: 2732709..2733738 (+ 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_2 | g4469 | g4469.t2 | isoform | g4469.t2 | 2730360 | 2731713 |
| chr_2 | g4469 | g4469.t2 | exon | g4469.t2.exon1 | 2730360 | 2730469 |
| chr_2 | g4469 | g4469.t2 | TSS | g4469.t2 | 2730368 | 2730368 |
| chr_2 | g4469 | g4469.t2 | exon | g4469.t2.exon2 | 2730637 | 2731713 |
| chr_2 | g4469 | g4469.t2 | cds | g4469.t2.CDS1 | 2730650 | 2731711 |
| chr_2 | g4469 | g4469.t2 | TTS | g4469.t2 | NA | NA |
Sequences
>g4469.t2 Gene=g4469 Length=1187
AGAATTCATTTGAGTGTAGAATTTTTCTGTAAATCTTTTGGGTAATTATTTTAATAATAA
AATTCAAGTGTAAATTAAGGCTTGAATTAAATTAATATTATATTGGTCAAAAAGTGTAAA
AGAATGTCGCCTGTATCAGGAGAAGAAAGTAGTGCAACTCAGTCAAATTTAAATGCCAAC
GCATCAGAATTTATTCCGATTATGATTAATGAAGAATCGACTCAATTAGCAACAACAAAT
TCAATTCATTCAACTACTGGTGCTATTCCCAAAAAATTTTATAAAAGTAACAATAATTAT
CGTCGTGATAAGTTTGATAGAAATCAAAGATGGAGATCTAATAATGGTAGTAGTAGTCAA
CGAAGAGAGACTTTTGCAGAACGTAATAATAGAAATGAAAATGCTAATTTCGAACCATTA
GAAAGTAATAACCAAAATAAAAAGTTCTTTGCTAATAATAAACCACCGAAACAAAATGAT
AGAATGAATGATCAAAATCAGTATGAAGGATCATCTCAAACAATTCAAAGACAAAATATT
TCACGACAGATTAAAAATGCACAAATGTCAAATAATAATAGATTGAAAAATAATAATCGA
TATGGAGAAAATGAAGTGCTTAGTGAAAGACAATATTACAATCGTCGTAACAATAATTAT
GGTCGAAATTATAATGGAATTCGATCTAATAATGAAAATCAGAAGAAAGAAGTTGAACAA
AATCAACAAGAAGAAGTTAATGAAAAGCCAACTACAAAAAATCGTCCAAAAAAACGTGAA
CCGTTTAATCGTAAAAAGGATGAATCAAAAGCTTCAAGTGCTTCACAACGTGATCGATTG
ATAAAAGAAATTGAATCAAATACATTAGAGTGCATGATATGTTGTGAAAAGATTAAGTCT
TATCAACCAATTTGGAGTTGCTCAAACTGTTATCACATTCTTCACTTATATTGTATCAAA
ACTTGGATGAAAAATTCAAAAAATGATGAAGGTGAATGGAGATGCCCAGCATGTAATCAA
ATGACAAATCAAAAGCCTGGTGATTATTTATGTTTTTGTGGTAAACTTAAAAATCCAGCT
GTAAATCGCAATGATCTAGCTCATTCATGTGGTGAAATGTGTATGAATCAAACACTTTGT
CCACATCCTTGTCAATTAAAATGTCATCCAGGTCCGCATGAAATTTG
>g4469.t2 Gene=g4469 Length=354
MSPVSGEESSATQSNLNANASEFIPIMINEESTQLATTNSIHSTTGAIPKKFYKSNNNYR
RDKFDRNQRWRSNNGSSSQRRETFAERNNRNENANFEPLESNNQNKKFFANNKPPKQNDR
MNDQNQYEGSSQTIQRQNISRQIKNAQMSNNNRLKNNNRYGENEVLSERQYYNRRNNNYG
RNYNGIRSNNENQKKEVEQNQQEEVNEKPTTKNRPKKREPFNRKKDESKASSASQRDRLI
KEIESNTLECMICCEKIKSYQPIWSCSNCYHILHLYCIKTWMKNSKNDEGEWRCPACNQM
TNQKPGDYLCFCGKLKNPAVNRNDLAHSCGEMCMNQTLCPHPCQLKCHPGPHEI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4469.t2 | CDD | cd16696 | RING-CH-C4HC3_NFX1 | 249 | 298 | 1.41869E-20 |
| 5 | g4469.t2 | Coils | Coil | Coil | 183 | 208 | - |
| 4 | g4469.t2 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 219 | 306 | 1.6E-9 |
| 9 | g4469.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 105 | - |
| 13 | g4469.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 55 | 69 | - |
| 8 | g4469.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 89 | 105 | - |
| 11 | g4469.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 238 | - |
| 12 | g4469.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 146 | 190 | - |
| 10 | g4469.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 191 | 238 | - |
| 1 | g4469.t2 | PANTHER | PTHR12360:SF12 | TRANSCRIPTIONAL REPRESSOR NF-X1 | 105 | 352 | 3.1E-45 |
| 2 | g4469.t2 | PANTHER | PTHR12360 | NUCLEAR TRANSCRIPTION FACTOR, X-BOX BINDING 1 NFX1 | 105 | 352 | 3.1E-45 |
| 7 | g4469.t2 | ProSitePatterns | PS01359 | Zinc finger PHD-type signature. | 250 | 297 | - |
| 15 | g4469.t2 | ProSiteProfiles | PS50016 | Zinc finger PHD-type profile. | 247 | 300 | 9.179 |
| 14 | g4469.t2 | ProSiteProfiles | PS50089 | Zinc finger RING-type profile. | 250 | 298 | 11.014 |
| 3 | g4469.t2 | 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.
