General information for g560.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g560 is located on chr_3: 4051404..4052776 (- 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_3 | g560 | g560.t1 | TTS | g560.t1 | 4051144 | 4051144 |
| chr_3 | g560 | g560.t1 | isoform | g560.t1 | 4051404 | 4052776 |
| chr_3 | g560 | g560.t1 | exon | g560.t1.exon1 | 4051404 | 4051412 |
| chr_3 | g560 | g560.t1 | cds | g560.t1.CDS1 | 4051404 | 4051412 |
| chr_3 | g560 | g560.t1 | exon | g560.t1.exon2 | 4051467 | 4051581 |
| chr_3 | g560 | g560.t1 | cds | g560.t1.CDS2 | 4051467 | 4051581 |
| chr_3 | g560 | g560.t1 | exon | g560.t1.exon3 | 4051640 | 4052100 |
| chr_3 | g560 | g560.t1 | cds | g560.t1.CDS3 | 4051640 | 4052100 |
| chr_3 | g560 | g560.t1 | exon | g560.t1.exon4 | 4052159 | 4052474 |
| chr_3 | g560 | g560.t1 | cds | g560.t1.CDS4 | 4052159 | 4052474 |
| chr_3 | g560 | g560.t1 | exon | g560.t1.exon5 | 4052526 | 4052776 |
| chr_3 | g560 | g560.t1 | cds | g560.t1.CDS5 | 4052526 | 4052776 |
| chr_3 | g560 | g560.t1 | TSS | g560.t1 | NA | NA |
Sequences
>g560.t1 Gene=g560 Length=1152
ATGGAAAGAAATCTTACGTGTTTCATAGCAAATGATCTTGGCAATCATATTCATATAGAG
AAAGAGTTAAATGTATTTAAGAAGATTGAATGGAAATTAGAGAATTTTTTAAAATTTAAA
GAAGATTCAAATCAATTTGGGAAACTTTATCATGAATTGGATGAAGAAGGATTTGAAGTA
AATTTTGATTTAGAACCAGCAATAAAGGACAAAGTTTTATTAAAATATTGTGATCATATG
AGTATTGTTATTGATTTGACGTTGGAAAACACGTTTGGTTTGAGAGTTTATATTTGTGCA
AAATTAATTAAAAACATGAACACAACTGATCTCTGTGAATGCAATATACTTGATAAGTTC
GAATGTTGCGAATGCGATGAATGTTACACATATAAATTTACAAAACACAAATGCTACATC
AAATTGAACAATGAATTATATGAACTTATATTCGACGATATGTGTGACGAGCCTGAATTT
GATGAAGACGAACCGATTGAACATACATGGTGTCTTTATGATGATGATCTGAAGCTTGAT
GACGATGTGCTTGTGATTGATCTTCATCTAAATTTCAATTATAAAATAATGCAATGCATT
CAATCACATCCATATGAAGATTATCTTGGTGATAAGAATTTCAATGAGCTAAAAATTATT
TGTTCTGATGGCATTATACTTTATGCAAACCGATTAATTTTGGCTATGAATTCTTCTGTT
TTTAGAACAATGTTTCAGACAAATATGATTGAGAGCGAAATGAAAGAAGTTGTTGTAAAC
GACATTGATTCAAAAACTATGCAAGAATTTTTACGCTTTGCTTATAGTAGCAAAATTGAA
AATTTAGATTATGTTGCTGAATCATTATTATACTGTGCTGAAAAATACGAAGTAAATGAT
CTCAAGAATACATGCATCGCACATCTTATCAAGAATTTGAAGAAGGATAATGTTTTTGAA
ATTTTGCAACTGGCTGAAATGCTAAACTTGAAAATAATGATGAATCAATGTTTGAATTTT
ATCTGCAAATCATTTGAAAAAGTAGAAGATGTCAATGAATTCGATAGATTGAATGAAAGT
TTGAAAAAGAAAGTAATTGAAGGAAAATGTAAAATGTTTATCGAGCCCATTACAACTTAT
GTTCCTAAATGA
>g560.t1 Gene=g560 Length=383
MERNLTCFIANDLGNHIHIEKELNVFKKIEWKLENFLKFKEDSNQFGKLYHELDEEGFEV
NFDLEPAIKDKVLLKYCDHMSIVIDLTLENTFGLRVYICAKLIKNMNTTDLCECNILDKF
ECCECDECYTYKFTKHKCYIKLNNELYELIFDDMCDEPEFDEDEPIEHTWCLYDDDLKLD
DDVLVIDLHLNFNYKIMQCIQSHPYEDYLGDKNFNELKIICSDGIILYANRLILAMNSSV
FRTMFQTNMIESEMKEVVVNDIDSKTMQEFLRFAYSSKIENLDYVAESLLYCAEKYEVND
LKNTCIAHLIKNLKKDNVFEILQLAEMLNLKIMMNQCLNFICKSFEKVEDVNEFDRLNES
LKKKVIEGKCKMFIEPITTYVPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g560.t1 | CDD | cd18186 | BTB_POZ_ZBTB_KLHL-like | 219 | 296 | 0.000e+00 |
| 8 | g560.t1 | CDD | cd14733 | BACK | 316 | 367 | 1.730e-05 |
| 6 | g560.t1 | Gene3D | G3DSA:3.30.710.10 | Potassium Channel Kv1.1; Chain A | 204 | 350 | 0.000e+00 |
| 2 | g560.t1 | PANTHER | PTHR24413:SF213 | FI01029P-RELATED | 23 | 352 | 0.000e+00 |
| 3 | g560.t1 | PANTHER | PTHR24413 | SPECKLE-TYPE POZ PROTEIN | 23 | 352 | 0.000e+00 |
| 1 | g560.t1 | Pfam | PF00651 | BTB/POZ domain | 212 | 312 | 0.000e+00 |
| 7 | g560.t1 | ProSiteProfiles | PS50097 | BTB domain profile. | 215 | 283 | 1.537e+01 |
| 5 | g560.t1 | SMART | SM00225 | BTB_4 | 215 | 313 | 0.000e+00 |
| 4 | g560.t1 | SUPERFAMILY | SSF54695 | POZ domain | 207 | 311 | 0.000e+00 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g560/g560.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g560.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein 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. There were no conditions that were differentially expressed