General information for g5412.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5412 is located on chr_2: 9440591..9442504 (- 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 | g5412 | g5412.t1 | isoform | g5412.t1 | 9440591 | 9442504 |
| chr_2 | g5412 | g5412.t1 | exon | g5412.t1.exon1 | 9440591 | 9441044 |
| chr_2 | g5412 | g5412.t1 | cds | g5412.t1.CDS1 | 9440591 | 9441044 |
| chr_2 | g5412 | g5412.t1 | exon | g5412.t1.exon2 | 9441102 | 9442504 |
| chr_2 | g5412 | g5412.t1 | cds | g5412.t1.CDS2 | 9441102 | 9442504 |
| chr_2 | g5412 | g5412.t1 | TSS | g5412.t1 | NA | NA |
| chr_2 | g5412 | g5412.t1 | TTS | g5412.t1 | NA | NA |
Sequences
>g5412.t1 Gene=g5412 Length=1857
ATGTTATTGCATTTGCTTCTTATTTCTTCGAAAATTCCAGGAGCTTTCACATTGTTAAAA
GATTTTCCTTTGCCAAAATATAGCAGTGCATTGTCATTTGCTGTTATTGATATAATTCAA
GATTTTTATGTGCAAGATACAAATACAATTAATATCTATCAAGTGGGTAAAGATGAAAAA
GCAGAGACAAAAAATTATGACATTATCAATGAAATTCTCTATCATGTGAAACTAATGGAA
GTTGTCGTAAGATTAGAAAATTTTTATGACGTGAAGGAGGTGAAAAAGAAACGAGCACAT
AATTTAATTTTTGTTGATAATTTTCAATCATTTATGTGCTTTTTTAATGCAATTTCTTCT
TATGATTTTGAATTTCAAGGATTTTTCCTAATTATTTTAACAACTTATTCATACGAGCAG
TATACAGTAATGTCAAATATTTTTGCTTTTTTATGGAATGAATACATTACAAATGTCAAT
ATCGTTTGGGAAACATCAGAAAATGAAGCTATAATGTACACTTATTTTCCTTACACAAAT
TTCTACTGTGGAAAATCGATTCCAGTTCAATTAAATCAATTTTCTTTTGGCAAATGGTTA
CAAAATCATTCAAGCATTTTTCCAGAAAAAATGACAAACCTTCATAGATGCCCATTGAGT
GCTGCAATAGTTTTAACAGGTCCATTTATGAGTCTTCTCAATGTTAGCAATGACACAGTG
AATCCCGATGGAATTGATGGTGTTCTTCTTCGTGTCATTTCACAAAGAATGAATTTCACT
CTCAAATTAGTATTGTGTTTAGATCAAGGAATGTTTTATGAAAATGGAACGATTGATGGT
GCTGCAAAGTTGGTCATTGATAGAGAAGTGAATATGACCATTGGCTATACACCTATGTCA
TCTGAAAGAAATTATTTTATGATGCCATCTTACATTTACCACACTTCAAATCTCATTTGG
ATTGTTCCACCTGGGCGACTTTTAAGTTCAATGGAAAAATTAGGAAAACCATTTGGATTG
CTTTTATGGATTTTTGTCTCATTAATTTTTATTGTCAGCTTTTTCACTGTGATTGCTTTA
AAATTTCAATCAAAAATTGTTCAAAATTTTGTTTTTGGTCGTGAAATTTCAACACCATCG
CTCAACATTTTGAATGTATTTTTCGGCAATTCACTTCATAAATTACCAAAAAGAAATTTT
GCAAGATTTATTTTGGGATTCTTCATGTTTTACTGTCTAGTCATCAGAAGTTCTTACCAA
GGTGCACTTTTTAATTTTATGCGAGGTGATTTTAGAGAAAGCCATGTAAAAACTATTGAA
GCAATGGCAAAAAGAGATTTTAAGTTTCATGTTGTTAAATCTTCACTTGATTCAGTTCAT
GAATTGCCTGAAGTTATGAACAGAATTTCAATAATTGAGCGTGGAGATTTTCCTAAAATA
AAAGATAAACTTATGGATTCAAATTACAAAGCAGGAGTTTTAGGTTCAGAAGAGCATGTA
GCTTGGTTAAATCAAAAAGAAACACCAGAAAAATTTTATCATTACACTGAAGAAGTTGTT
TCAGTTTTCAATCTTTGTATTTATATGCATCGACAAACTTGCCTTGCACATAATGTTAAT
GAAAACATCATAAAACTTACAAATAGCGGCTTAATGGAATCATGGAAGAAAAAGTTTGTT
GATAGATCTTATTTGAAATTAAGAATTAATGAAGAGCCAAAGCAGTTAGATAATGAAAAG
TTGGCAGGAGCTTATAAGCTTCTAATTTATGGATTAATAATCAGTTTTATTGTGTTTATT
GTCGAGTTAATTTCCTTTAGATTCAAATGTCTGCATCGCGTGATGATAAACTTTTAA
>g5412.t1 Gene=g5412 Length=618
MLLHLLLISSKIPGAFTLLKDFPLPKYSSALSFAVIDIIQDFYVQDTNTINIYQVGKDEK
AETKNYDIINEILYHVKLMEVVVRLENFYDVKEVKKKRAHNLIFVDNFQSFMCFFNAISS
YDFEFQGFFLIILTTYSYEQYTVMSNIFAFLWNEYITNVNIVWETSENEAIMYTYFPYTN
FYCGKSIPVQLNQFSFGKWLQNHSSIFPEKMTNLHRCPLSAAIVLTGPFMSLLNVSNDTV
NPDGIDGVLLRVISQRMNFTLKLVLCLDQGMFYENGTIDGAAKLVIDREVNMTIGYTPMS
SERNYFMMPSYIYHTSNLIWIVPPGRLLSSMEKLGKPFGLLLWIFVSLIFIVSFFTVIAL
KFQSKIVQNFVFGREISTPSLNILNVFFGNSLHKLPKRNFARFILGFFMFYCLVIRSSYQ
GALFNFMRGDFRESHVKTIEAMAKRDFKFHVVKSSLDSVHELPEVMNRISIIERGDFPKI
KDKLMDSNYKAGVLGSEEHVAWLNQKETPEKFYHYTEEVVSVFNLCIYMHRQTCLAHNVN
ENIIKLTNSGLMESWKKKFVDRSYLKLRINEEPKQLDNEKLAGAYKLLIYGLIISFIVFI
VELISFRFKCLHRVMINF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g5412.t1 | Gene3D | G3DSA:3.40.190.10 | - | 249 | 574 | 3.3E-30 |
| 9 | g5412.t1 | Gene3D | G3DSA:3.40.190.10 | - | 317 | 525 | 3.3E-30 |
| 8 | g5412.t1 | Gene3D | G3DSA:1.10.287.70 | - | 326 | 602 | 3.3E-30 |
| 1 | g5412.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 91 | 612 | 3.0E-61 |
| 2 | g5412.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 91 | 612 | 3.0E-61 |
| 15 | g5412.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 14 | - |
| 16 | g5412.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 17 | g5412.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 9 | - |
| 21 | g5412.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 10 | 14 | - |
| 14 | g5412.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 15 | 339 | - |
| 18 | g5412.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 340 | 360 | - |
| 11 | g5412.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 361 | 399 | - |
| 20 | g5412.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 419 | - |
| 13 | g5412.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 420 | 586 | - |
| 19 | g5412.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 587 | 606 | - |
| 12 | g5412.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 607 | 618 | - |
| 6 | g5412.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 235 | 561 | 4.24E-17 |
| 7 | g5412.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 17 | - |
| 3 | g5412.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 338 | 360 | - |
| 5 | g5412.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 419 | - |
| 4 | g5412.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 587 | 606 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5412/g5412.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5412.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