General information for g5738.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g5738 is located on chr_2: 11464612..11466662 (- 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 | g5738 | g5738.t1 | isoform | g5738.t1 | 11464612 | 11466662 |
| chr_2 | g5738 | g5738.t1 | exon | g5738.t1.exon1 | 11464612 | 11465110 |
| chr_2 | g5738 | g5738.t1 | cds | g5738.t1.CDS1 | 11464612 | 11465110 |
| chr_2 | g5738 | g5738.t1 | exon | g5738.t1.exon2 | 11465205 | 11465640 |
| chr_2 | g5738 | g5738.t1 | cds | g5738.t1.CDS2 | 11465205 | 11465640 |
| chr_2 | g5738 | g5738.t1 | exon | g5738.t1.exon3 | 11465696 | 11466662 |
| chr_2 | g5738 | g5738.t1 | cds | g5738.t1.CDS3 | 11465696 | 11466662 |
| chr_2 | g5738 | g5738.t1 | TSS | g5738.t1 | NA | NA |
| chr_2 | g5738 | g5738.t1 | TTS | g5738.t1 | NA | NA |
Sequences
>g5738.t1 Gene=g5738 Length=1902
ATGAATAACAAAGGAATTATCATTTTGTTCATAATTTCAACAATTGATTCATCGAATTCT
TTCAATATCATTTTAAATAATCAAACAGAAGACCTTGTAACTGCTTCTGCAATTATAGTC
AACAAACTTTATTTACCAATTCTTTCACATATAACAATTGTTCATTCAATCAGTAAAGAA
AATTCCCAAAAATTCTCTGACACTTTCACAAGTTTCATAACAATAGTGAAAACAAATTTA
ACCTACCAAATTGAAAATGTGATTTCACTCAAGCAAATATTTGACAAACGAAGATCAAAT
TTAATTTTTATTGACTCACTTGAATCATTCAAAACAGTTTGTGAACATCTTAATCAAAAT
TACTTCAAACTGCGCAAATTATTTACAGTGATTTCAATCAACATTCTAAAAGAAACAGAA
ATGGAAGGCATTTTTGATTGCTTCATGAAACGCTTAGTAATTGACACAAATATCATCACA
TATGATGAAAATAAAACTGTCAATTTATTTACATTTTTTCCTTATCGAAATGAAAATGAG
TGCAGTAATATAAAACCGATTAAAATTAATTCATTCAATAGCAGCATTGAACAATGGAAT
AATGATAAATTTTATATTAGAAGATCTAATGATCTTAAAAAGTGTTTATTACATATTGGT
TCAGCAGCTGTCGCAGCCGAACCTGCTGTTATCCTTAAAAATAACTCAAAAGGCGCTCTA
CAAGTTGCAGGCATTGAAAAAGATATTTTTATTGAACTCGCACATCGCCTCAATTTCACG
CCTAATTTTGTGATCTATTTGGAGTCAGTTGGATCGATTTTTAGTAATGGAACAGGGAAA
GGAGTTTTGGGAAAAGTTCTAGAAGGCAAAGTTGATGCTGCAATTGGATTTGTAACATTA
CAGTATGAAAGAGCTATGTTTTTAAGTGAAACTACAGCTTATGCGATGCATCCACTTGCG
CTAATTATTCCTAATGGTGAAGAATATGGTGACATGGAAAAACTTTTACGACCTTTTACA
GCAATTGTTTGGAGAATTCTTTTTATAATTTTATTATTTTCATCATTTTTTGCTCTTATT
TTTCTTAAATTTCCTAAAATTTACAATTTTGTATTTGGTCGGGGAGTTAACCATCCATTG
AGTATTATTATCGCAATACACTTGGGAGTTCCACAACCAAGATTGCCAAAGAGAAATTTT
GCAAGATTTATTTTGTTGAATTTTCTTGCTTACTGTCTTGTTGTGCGTTCTTCTTATCAA
GGAGCTGTCTTTAATATATTAATGTCAAATGATCGCAAACCACCAGTAGCGTCAATTAAT
GAAATTATGGATAAACGCTACACTTTTTATATTTATGAATCACTTTCAAGTCGAGTGCAA
GGATTGTTAATTGCCTATAAAAACCATAAAATCTTTCCAAATGCTGACATTGACAAATAT
AGACGAAAAACATTAGAACAAAATTTTCGTGGAGTAGTTTTCAACTATGAAAATCAAATT
CATTATCTCAATCAATTGAATTATAAAAAATTCACTTATACAATATGCAAGGAACACTTT
CTTGTTCCATCATTTGTATTCTATTTTCGAAAAAATCACTTTTTAATAGGAGAAGTAAAT
TCTTATATTGAAAGAATGCTTGCAAATGGTCTAATTGAATTCATTTCATCAAAATATGCC
GACAAAGATTATTTGAAGATGAAGCCGGATGAAGCACCGAAGGTCTTACAGATTAAACAT
ATTTATGGTGCAATTGAACTCTATTTCCTCTGCAATTGCGTTTCGGTTGTCATTTTCATA
ATGGAATTAGCAACAAAACTGAAACATTCTTTGAGATTTCCAAAGATAAGAGCAAAAAGA
AGATCAAGAATTTCCATTGTTAGACCCGAGCATGCTCGTTGA
>g5738.t1 Gene=g5738 Length=633
MNNKGIIILFIISTIDSSNSFNIILNNQTEDLVTASAIIVNKLYLPILSHITIVHSISKE
NSQKFSDTFTSFITIVKTNLTYQIENVISLKQIFDKRRSNLIFIDSLESFKTVCEHLNQN
YFKLRKLFTVISINILKETEMEGIFDCFMKRLVIDTNIITYDENKTVNLFTFFPYRNENE
CSNIKPIKINSFNSSIEQWNNDKFYIRRSNDLKKCLLHIGSAAVAAEPAVILKNNSKGAL
QVAGIEKDIFIELAHRLNFTPNFVIYLESVGSIFSNGTGKGVLGKVLEGKVDAAIGFVTL
QYERAMFLSETTAYAMHPLALIIPNGEEYGDMEKLLRPFTAIVWRILFIILLFSSFFALI
FLKFPKIYNFVFGRGVNHPLSIIIAIHLGVPQPRLPKRNFARFILLNFLAYCLVVRSSYQ
GAVFNILMSNDRKPPVASINEIMDKRYTFYIYESLSSRVQGLLIAYKNHKIFPNADIDKY
RRKTLEQNFRGVVFNYENQIHYLNQLNYKKFTYTICKEHFLVPSFVFYFRKNHFLIGEVN
SYIERMLANGLIEFISSKYADKDYLKMKPDEAPKVLQIKHIYGAIELYFLCNCVSVVIFI
MELATKLKHSLRFPKIRAKRRSRISIVRPEHAR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5738.t1 | Gene3D | G3DSA:3.40.190.10 | - | 243 | 574 | 3.1E-28 |
| 10 | g5738.t1 | Gene3D | G3DSA:3.40.190.10 | - | 318 | 525 | 3.1E-28 |
| 9 | g5738.t1 | Gene3D | G3DSA:1.10.287.70 | - | 328 | 602 | 3.1E-28 |
| 2 | g5738.t1 | PANTHER | PTHR42643:SF16 | IONOTROPIC RECEPTOR 11A-RELATED | 9 | 607 | 3.2E-52 |
| 3 | g5738.t1 | PANTHER | PTHR42643 | IONOTROPIC RECEPTOR 20A-RELATED | 9 | 607 | 3.2E-52 |
| 1 | g5738.t1 | Pfam | PF00497 | Bacterial extracellular solute-binding proteins, family 3 | 240 | 560 | 3.8E-6 |
| 14 | g5738.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 341 | - |
| 18 | g5738.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 342 | 361 | - |
| 16 | g5738.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 362 | 366 | - |
| 20 | g5738.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 367 | 388 | - |
| 13 | g5738.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 389 | 399 | - |
| 19 | g5738.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 419 | - |
| 15 | g5738.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 420 | 586 | - |
| 17 | g5738.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 587 | 605 | - |
| 12 | g5738.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 606 | 633 | - |
| 8 | g5738.t1 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II | 215 | 563 | 6.08E-21 |
| 6 | g5738.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 342 | 364 | - |
| 5 | g5738.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 371 | 390 | - |
| 7 | g5738.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 419 | - |
| 4 | g5738.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 582 | 604 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5738/g5738.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5738.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