General information for g4469.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t8 | isoform | g4469.t8 | 2732709 | 2733738 |
| chr_2 | g4469 | g4469.t8 | exon | g4469.t8.exon1 | 2732709 | 2733738 |
| chr_2 | g4469 | g4469.t8 | cds | g4469.t8.CDS1 | 2732798 | 2733610 |
| chr_2 | g4469 | g4469.t8 | TTS | g4469.t8 | 2733717 | 2733717 |
| chr_2 | g4469 | g4469.t8 | TSS | g4469.t8 | NA | NA |
Sequences
>g4469.t8 Gene=g4469 Length=1030
CATGTGTATTTTTGACAAGTAAATTCTGTTATGGAAAACATGAAGAACGAAAGACAATTC
CTTGCAACCAAGAGTCTTTCTGTTGTGGAATGCCATGCGGCAAATTATTGAAATGTGGTC
GGCATACTTGTATTAAAACATGTCATCAAGGAGAATGTGAGAAAAAGGATGATTTTTGCA
AGCAAAAATGTACAATGAAACGATTTGAGTGTGATCACAATTGTAATGCACAATGTCATG
AAGGAAAATGTCCGGACAATATATCTTGTCGTGAAAAAGTTCAAGTTTCATGTGTATGTG
GAAATCTCAAAGAATTCAAGACATGCGAACAAGTTGAATATGAGAATAAAAAACTTCAAA
GAATTCACATTACTATGCAAATGCAAGAAATGCAACAAAGTGATGGAATAACTGATCTTA
AAACAATGCTTGGTGATTTCAAAAAGACTACGAAAATTCTTGAATGTAATGATGAATGCA
AGACTTTAGAGCGAAATCGTCGTCTTGATATTGCATTCAAAGTTCAAAATCCAACACTTG
CTTCTACACCTCGATTCGTTCCTACCTATAGTGATCACGTTCGAAATTATTATAAAAAAG
ATCCAACTTTCGTTAATATGGTGCATGATAAATTGACTGAGTTAGTAAAATTAGCAAAAG
AAAGTAAAGCTCCATATCGTTGTCATTCATTTCCTTCAATGAATCGTGATAAGCGTCATG
TTATACATGACATGGCAGAATTATTTGGTATTGAAACGCAAGCTTATGATGCTGAACCTA
ATCGAAATATTGTTGCAACAGCTACACGAGAATATTGTTGGCTTCCATCAATGAGTATGG
CTGAAATTGCTAGTCGCGAAAATGGAGCTCGTCGACCGCCATCAAATCAAACTTTTAAAT
GATTAATGCCTTGAAAAATTTTTCTCTTTTATTTTTATTGCGTTTTTACATTTTCTTGAA
ATCATTTTATGATGAATAAATGCATGTATGAGAATGTTTCTCATGAAACTAAAATTATTT
ATGTTTTATT
>g4469.t8 Gene=g4469 Length=270
MPCGKLLKCGRHTCIKTCHQGECEKKDDFCKQKCTMKRFECDHNCNAQCHEGKCPDNISC
REKVQVSCVCGNLKEFKTCEQVEYENKKLQRIHITMQMQEMQQSDGITDLKTMLGDFKKT
TKILECNDECKTLERNRRLDIAFKVQNPTLASTPRFVPTYSDHVRNYYKKDPTFVNMVHD
KLTELVKLAKESKAPYRCHSFPSMNRDKRHVIHDMAELFGIETQAYDAEPNRNIVATATR
EYCWLPSMSMAEIASRENGARRPPSNQTFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4469.t8 | CDD | cd06008 | NF-X1-zinc-finger | 2 | 45 | 0.0000002 |
| 10 | g4469.t8 | CDD | cd02643 | R3H_NF-X1 | 165 | 238 | 0.0000000 |
| 8 | g4469.t8 | Gene3D | G3DSA:3.30.1370.50 | - | 167 | 261 | 0.0000000 |
| 2 | g4469.t8 | PANTHER | PTHR12360:SF12 | TRANSCRIPTIONAL REPRESSOR NF-X1 | 2 | 243 | 0.0000000 |
| 3 | g4469.t8 | PANTHER | PTHR12360 | NUCLEAR TRANSCRIPTION FACTOR, X-BOX BINDING 1 NFX1 | 2 | 243 | 0.0000000 |
| 1 | g4469.t8 | Pfam | PF01424 | R3H domain | 173 | 237 | 0.0000000 |
| 9 | g4469.t8 | ProSiteProfiles | PS51061 | R3H domain profile. | 172 | 240 | 13.4780000 |
| 7 | g4469.t8 | SMART | SM00438 | znfxneu3 | 9 | 32 | 0.0051000 |
| 6 | g4469.t8 | SMART | SM00438 | znfxneu3 | 41 | 62 | 0.0230000 |
| 5 | g4469.t8 | SMART | SM00393 | R3H_4 | 163 | 239 | 0.0000034 |
| 4 | g4469.t8 | SUPERFAMILY | SSF82708 | R3H domain | 148 | 261 | 0.0000000 |
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:0005634 | nucleus | CC |
| GO:0008270 | zinc ion binding | MF |
| GO:0003700 | DNA-binding transcription factor activity | MF |
| GO:0003676 | nucleic acid 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.
