General information for g5458.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5458 is located on chr_2: 9679335..9698759 (- 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 | g5458 | g5458.t4 | TTS | g5458.t4 | 9677650 | 9677650 |
| chr_2 | g5458 | g5458.t4 | isoform | g5458.t4 | 9677666 | 9679335 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon1 | 9677666 | 9677829 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon2 | 9677960 | 9678407 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon3 | 9678464 | 9678514 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon4 | 9678608 | 9678663 |
| chr_2 | g5458 | g5458.t4 | cds | g5458.t4.CDS1 | 9678638 | 9678663 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon5 | 9678733 | 9678753 |
| chr_2 | g5458 | g5458.t4 | cds | g5458.t4.CDS2 | 9678733 | 9678753 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon6 | 9678820 | 9678942 |
| chr_2 | g5458 | g5458.t4 | cds | g5458.t4.CDS3 | 9678820 | 9678942 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon7 | 9679004 | 9679210 |
| chr_2 | g5458 | g5458.t4 | cds | g5458.t4.CDS4 | 9679004 | 9679210 |
| chr_2 | g5458 | g5458.t4 | exon | g5458.t4.exon8 | 9679278 | 9679335 |
| chr_2 | g5458 | g5458.t4 | cds | g5458.t4.CDS5 | 9679278 | 9679335 |
| chr_2 | g5458 | g5458.t4 | TSS | g5458.t4 | 9679356 | 9679356 |
Sequences
>g5458.t4 Gene=g5458 Length=1128
ATGAAAAGAATAATAATCATTGAGTTTGTGATTTTTACGGTGGTTTGGGGTCAAACACCA
TGCACCGTTTCAAAGACAAAACAAGTAGGTGAGTGCATGTTCATTAGTAACTGCCCTGAG
GTTCTTAAAACTTTCAAAGAATCTGGTGAAATGCCGACAATATGTGACCGTGTTCTGCGT
ACTATTTGTTGTCCTTTAAAAACCACTACAACGTCTACAACTACAACAACAACTACTCAT
TCACCTATTCGTATAAGTGTCAAAAAATGTAAAGAATATGGTCAACTGGTGTATGAAAAA
AAAATTGTAAACAGTTCAATTATTGGCGAACCAAGTGTCGTTAAAATGATATCAAAGTGT
AATCACGAATCAGTGCCACTTATTGTTGGTGGTGAAGATGCAAAGGATGAGGGGAATTCC
CTCACATGGCGTTAATAGGGTTTGGGGATGGCAATAGAATGGAAGATTATCAATGTGGAG
GTTCGATGATTTCTGAACAGTGGATTCTCTCAGTATGCGGCTCATTGTGTCAGTACTGGT
GGTTTAACAGCAAATTTTGCAAAAGTTGGTAATGTGGTTCGAGGACGAGACACATTGAAT
TCATGGACTTATAAAATAATTCAAAGAATTCCTCATCCAAATTATAATTCAAGATTTGCA
GATGATGATATTGCATTATTTAAACTTGAAAAACCTGCACAATTAAATGTTCATGTTATA
CCAATTTGTTTACCAGATAAAGAATTACTTACTACAAAATCAGCTATAGCAAGTGGCTAT
GGACGTACTGGATTTGCTGATGATGTTAGTGAAAAATTGATGAAAGTTATAATTGAATAT
TTTAAGCCAGCAGATTGTAATGAAGCATTTGCGGATAACACAAAACTTTCAAATAATCAA
ATAAATTGGGATAAAATGGTTTGTGCGGGGTCTCATAATAAAACTGGTGACACTTGTAAT
GTAAGTCCATTGCAAATTTATCATTCTGATGTCTATTGCATGTATAAAATAATTGGTATC
ACATCCTTTGGTCATGCTTACTGCGGTTTTCCTGGTGTCCCTGCTATTTATACAAAGGTC
TATCACTATTTAGATTGGATTGAATCTATTGTTTGGCCAAATCAATAA
>g5458.t4 Gene=g5458 Length=144
MKRIIIIEFVIFTVVWGQTPCTVSKTKQVGECMFISNCPEVLKTFKESGEMPTICDRVLR
TICCPLKTTTTSTTTTTTTHSPIRISVKKCKEYGQLVYEKKIVNSSIIGEPSVVKMISKC
NHESVPLIVGGEDAKDEGNSLTWR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5458.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 17 | - |
| 4 | g5458.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 5 | g5458.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 6 | g5458.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 17 | - |
| 2 | g5458.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 18 | 144 | - |
| 1 | g5458.t4 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5458/g5458.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5458.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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