General information for g5411.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5411 is located on chr_2: 9438257..9440158 (- 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 | g5411 | g5411.t1 | isoform | g5411.t1 | 9438257 | 9440158 |
| chr_2 | g5411 | g5411.t1 | exon | g5411.t1.exon1 | 9438257 | 9440158 |
| chr_2 | g5411 | g5411.t1 | cds | g5411.t1.CDS1 | 9438257 | 9440158 |
| chr_2 | g5411 | g5411.t1 | TSS | g5411.t1 | NA | NA |
| chr_2 | g5411 | g5411.t1 | TTS | g5411.t1 | NA | NA |
Sequences
>g5411.t1 Gene=g5411 Length=1902
ATGCTGAAATTACTCATTTTTCTGCTTTTAATAAATGTTTCAGCTAGTGAAATTAAAGAT
TTTTCAATGCCAAACTACAGCACAGCTGTGTCAAGAGTCATCATTGATTATATAAAGAAC
TTTTTTCTCAATGTCACGAATACAGTCAATTTCTACCAAATGTCACTTGAAAACAATTTA
AATGTGAATTTCGACATCATGAACGAAGTGTTGTACAATGTAAAAACAAAAACAGTTGTG
CAAGTTGATAGTTTCGAAGATTCAAAAATTTCAATTGTCAAACACTATGTGAACATCATT
TTCTTTGATTGTTTTGAATCTTTTGAGAAAATTTACAAGAAAATGACATTGAAGAAATTT
GATTATCAAGGATTCTTTTTAATTATTATCACAACACATATGAATGATATTTACAAAACA
ATGCATAGAATTTTTGATGCTCTTTGGGTGCATCATATTATTAATGCAAATATAATTTTT
ATGCCAGAAGAAAACAATAATGAAGCACTAATTTATACATTTTTTCCATATTCACGTTTC
TATTGCGAAAATGTCGTTCCTTTACAACTCAATCATTATCGAGGTCAAAAATGGATCAAT
AAAATCAATTATTTTCCACATAAATTGCAAAATTTTTATGGTTGTACACTTCGTGTTGCA
ACTTTTCCAAATCCGCCATTTATGATAATCAATCAAGATAAAATAACTGGTCAGGTGTCA
GTTGATGGTCTTGATGGTACAATGATTCGTGTTTTATCACAACATTTCAATTTTAATGTG
CAACTCTCACTTCCTGCTGAACTTTGGGGTGATATTTATGAAAATGGAACTACCACGGGT
GCAATAAAAATGGTCATAAATGAAGAAGTGAATATGACACTAGGTTTTTTCGCAACAAAT
CCATCTCGTGATGCAGTTATGAAGTCTGGGTATGTTTATTATACAACAAATCTTGTTTGG
ATTGTTCCTCCTGGAAAACCTCAAACTTCACTACAAAAACTTCTTAATCCTCTTGATACA
AATTTTTGGATTTTGTCATCTATAACAATTTTAATTGGACTTTTAGCAATTGCAATTTTA
AAAAAACAGAAAAAAATTGTTCAAAATTTTGTCTTTGGTACTTCTATGCAAAGTCCTGGA
ATGAATTTGATAAATATTATTTTTGGTGGATCATTACATCATTTGCCTAAGAGAAATTTT
GCAAGATTTCTCATGGGATTGTTTTTATTTTTTACATTCATACTTAGAAGTTGTTATACT
GGAGGTTTAGTGAAATTTATGCAAATGGATACAAGAGGAAAACGAGTGCTGTCAACAGCT
GAAATGTTGGAACATAATTTTACTTTTTATATGTATCCTTCATCAAGAAGTTACTTTCTT
GAAATGCCACAAATACTTGAGCGAACAAAGTTTGTAACTGCAAGTGAATTCAATTCAAAA
TTAAAGCAATTGACTGTTGATCCTTATTATGATGCAGCTTTTATTACATCTATTGGACAT
TTAGCTTATCGAAATTTGCTTGTTTTTCCTCATCGCTTTCATCATCATGCTCCTGAGGCA
CTTTATACATTAAATATTGTCATTTATATGCATAAAGAATCGTGTTTGGCTCTTCCTTTT
AATTCAGCAATTACAAATTTAGTTAATGGTGGATTAGTATCAAAATGGGCTTCAAAATGG
ATAAATGGAAAATATTTAAAAGAAATTGTTGATGAAAGTCCTGATCCATTGAGTATGATG
CAATTAGAAGGTTGTTTTCAGTTGCTTTATGTTGGATTAATAATGAGTTCATTTATTTTT
ATTATGGAAGTTTTTGTAAGTCATAAAAAAGGAATTAAATTAAAAATTTCTAAAAATATA
AAAACCATAAAAATAAATTTAAGGAAATATTTTTCCAATTGA
>g5411.t1 Gene=g5411 Length=633
MLKLLIFLLLINVSASEIKDFSMPNYSTAVSRVIIDYIKNFFLNVTNTVNFYQMSLENNL
NVNFDIMNEVLYNVKTKTVVQVDSFEDSKISIVKHYVNIIFFDCFESFEKIYKKMTLKKF
DYQGFFLIIITTHMNDIYKTMHRIFDALWVHHIINANIIFMPEENNNEALIYTFFPYSRF
YCENVVPLQLNHYRGQKWINKINYFPHKLQNFYGCTLRVATFPNPPFMIINQDKITGQVS
VDGLDGTMIRVLSQHFNFNVQLSLPAELWGDIYENGTTTGAIKMVINEEVNMTLGFFATN
PSRDAVMKSGYVYYTTNLVWIVPPGKPQTSLQKLLNPLDTNFWILSSITILIGLLAIAIL
KKQKKIVQNFVFGTSMQSPGMNLINIIFGGSLHHLPKRNFARFLMGLFLFFTFILRSCYT
GGLVKFMQMDTRGKRVLSTAEMLEHNFTFYMYPSSRSYFLEMPQILERTKFVTASEFNSK
LKQLTVDPYYDAAFITSIGHLAYRNLLVFPHRFHHHAPEALYTLNIVIYMHKESCLALPF
NSAITNLVNGGLVSKWASKWINGKYLKEIVDESPDPLSMMQLEGCFQLLYVGLIMSSFIF
IMEVFVSHKKGIKLKISKNIKTIKINLRKYFSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5411.t1 | Gene3D | G3DSA:3.40.190.10 | - | 242 | 575 | 2.8E-33 |
| 10 | g5411.t1 | Gene3D | G3DSA:3.40.190.10 | - | 317 | 526 | 2.8E-33 |
| 9 | g5411.t1 | Gene3D | G3DSA:1.10.287.70 | - | 327 | 603 | 2.8E-33 |
| 1 | g5411.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 85 | 610 | 3.4E-67 |
| 2 | g5411.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 85 | 610 | 3.4E-67 |
| 16 | g5411.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 17 | g5411.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 18 | g5411.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 11 | - |
| 22 | g5411.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 15 | - |
| 14 | g5411.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 341 | - |
| 20 | g5411.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 342 | 360 | - |
| 13 | g5411.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 361 | 402 | - |
| 19 | g5411.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 403 | 424 | - |
| 15 | g5411.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 425 | 587 | - |
| 21 | g5411.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 588 | 606 | - |
| 12 | g5411.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 607 | 633 | - |
| 7 | g5411.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 214 | 564 | 1.02E-18 |
| 8 | g5411.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 4 | g5411.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 341 | 360 | - |
| 6 | g5411.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 367 | 389 | - |
| 5 | g5411.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 404 | 426 | - |
| 3 | g5411.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 588 | 607 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5411/g5411.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5411.t1.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