General information for g9237.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Gram-negative bacteria-binding protein 1.
Parent gene
- The parent gene g9237 is located on chr_1: 1037294..1038840 (+ 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_1 | g9237 | g9237.t1 | TSS | g9237.t1 | 1034202 | 1034202 |
| chr_1 | g9237 | g9237.t1 | isoform | g9237.t1 | 1034287 | 1038840 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon1 | 1034287 | 1034410 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS1 | 1034287 | 1034410 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon2 | 1034518 | 1034742 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS2 | 1034518 | 1034742 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon3 | 1035113 | 1035244 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS3 | 1035113 | 1035244 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon4 | 1035314 | 1035550 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS4 | 1035314 | 1035550 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon5 | 1035619 | 1035744 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS5 | 1035619 | 1035744 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon6 | 1036586 | 1036813 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS6 | 1036586 | 1036813 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon7 | 1036925 | 1037294 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS7 | 1036925 | 1037294 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon8 | 1037362 | 1037531 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS8 | 1037362 | 1037531 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon9 | 1038026 | 1038216 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS9 | 1038026 | 1038216 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon10 | 1038277 | 1038471 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS10 | 1038277 | 1038471 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon11 | 1038525 | 1038633 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS11 | 1038525 | 1038633 |
| chr_1 | g9237 | g9237.t1 | exon | g9237.t1.exon12 | 1038737 | 1038840 |
| chr_1 | g9237 | g9237.t1 | cds | g9237.t1.CDS12 | 1038737 | 1038840 |
| chr_1 | g9237 | g9237.t1 | TTS | g9237.t1 | 1038920 | 1038920 |
Sequences
>g9237.t1 Gene=g9237 Length=2211
ATGGAGTGCTTTACGATAAATTTAATTTTTCTAATTATTTTCGCTCCAATAGTTTATGGA
TTTTCAGTTCCAACAGTCAACGTGAAACTTTTGAAACCGAAAGGAATTCAATTTTCGATA
CAAGAGAAGAGAGATGTTTTTAATGACGTTAGAATTTTTGTGTTCGCTTCAAAAAGTTTA
ATAAATAATTTAAAGTTTGTTGAGAGTGAATTGAAAAGAGATGTCAATGGTTTATGGACA
TATGAAACAACTAATGTTGATTTGACTGCTGATGACAGCATTGAATATTGGATGTATGTT
GAATGCAATAAGTTGGGTCGTTATGTCACTAATGTGATAAAAGTTGCTGACATTGACCAG
CAACAGTCAAATCAAAAGCTAAATCCCAGGTCAATAGTCATAACACCAACAGTAAACAAT
ACTTATCCCCAAATTAATGTCAAACGTTCAAAAACGGGTAACATTCGGTTCTACATTCAA
GATGAACAACACGAAAACGGTCCATTAACCAATGTCAAATTAATTATTTTTGCATCAAAA
CCCATCGCTAATAATTCAAAATTAATTGAAGTGCCACTCGTGAAAAATAATGATAATGGA
GTGTGGAGCTATGAACTCAAAAATACACCATTGACAGTTGATGATGAGATTGAATATTGG
TTGTCAACCGAAATGTATGGTTTGGGGTATTTTTCTAATAATATTATCAAATTACGAGAT
TTAGAAATTGATGATGGAAAATGGCAAAAAAGACAATTTGTTGCAGAAGGCATTTTTAAT
GAAACTTTTCCTATTGTTAATGTTGAAATGGTTGGAAATAATGGTTTAGTCATTTCTTTA
CAAGAAGAATACGATGAATTTAACGATGTCAGAATAACAATATTTTCCCCAAAAATTCTC
GTAAATAATGATTTACAATACACTGAGAATCAGCTGAAACGCGATGATAGTGGGTTATGG
ATTTACGAGATGCGAAATATCGCCCTAAAAAATGATGACATATTCGAGTATTGGATTTAT
GTTGAAAAGCCAAATGTTGGTTATTTTGCGAGCCAAAAATTCAGAGTTCAAGATATCGCA
CCATCATCACCCGTTGAGCAGCTTCCACCATCACCTGAGCAGCTTAAAATATCGACAACA
ACACCAATGCCATCGACATGCGAAGCTTCTGTCAGTACAGTTAATGGAAAATCAGTCGCA
TGCAGAAATTCCATTATTTTCAATGAAGATTTTAATTTGGATAATTTGAGATATTGGAGC
TTCGACACTAGATTTCCATTAGATGACGCAACGGCAGACGCAGAATTTTGCATATACGAG
AAGCGTGCAGAAACTTCATTTATACGAGATGGTTCGATGACATTAAAAGCTGAATCATTG
AAAAAGATTGCTGGATTTGATGATGCTCGTATAAGAATTGGAAGTTATAATTTAAAAGAG
CGATGCACACCCATCTCAAATGATGAACGTGAATGTTCGCGACAGGCTCAATTCGGTTAC
ATTCTGCCCCCAGTGACATCAGCATACTTGACAACACGCAGTAAATTCTCATTTATGTAC
GGACGAGTGGAAGCACGCTTGAGAGCACCAATTGGTGATTACTTGTATGCACAAATTACA
TTACAACCACAATTAAAACCAGAAGAAGCTGCAAATGATAGTAGTACTTCACAGCATTTA
AAAGTATTTTTCGCAAGAGGAAATGAACAACTGAAAGATGCTGATGAGGAAGTTGGTGGA
AGTCGTGTATATGGTGGAGCAATTCTTTCAAAAAACCCAAAAAATAATCTCAAATGGTTG
AAGAGCAAACAATTTCCCAATACGCATCTCGGAAACGACTTTCACATTTATGAGCTGTTA
TGGACGCCAACAGAAATCAGCCTATCCATCGATGGCATAAAGTACGGTTCATTAAGCAGC
AATTTACGAGACTCTGCGATGGTTGCGAAAATCAAATCGGCTGTAAATTGGGCCAACAAT
GGACCATTTGATAGAGAGCACTTTTTATCGATAAACCTGGGAGCGGGTAGTGTCAAGAAC
TTTTATTCAATCAACAATACCCTCGTGAATGGTGCGGAGTTTGAACCGAAGCCATGGAGC
GATACAGATCCCAGAGCAGAACGTAGTTTTTATATGGCACATGACAAATGGTATCCAACA
TGGAAAAAACCTTCACTTGAAGTCGACTATATAAAAATTTATTCTGTTTAA
>g9237.t1 Gene=g9237 Length=736
MECFTINLIFLIIFAPIVYGFSVPTVNVKLLKPKGIQFSIQEKRDVFNDVRIFVFASKSL
INNLKFVESELKRDVNGLWTYETTNVDLTADDSIEYWMYVECNKLGRYVTNVIKVADIDQ
QQSNQKLNPRSIVITPTVNNTYPQINVKRSKTGNIRFYIQDEQHENGPLTNVKLIIFASK
PIANNSKLIEVPLVKNNDNGVWSYELKNTPLTVDDEIEYWLSTEMYGLGYFSNNIIKLRD
LEIDDGKWQKRQFVAEGIFNETFPIVNVEMVGNNGLVISLQEEYDEFNDVRITIFSPKIL
VNNDLQYTENQLKRDDSGLWIYEMRNIALKNDDIFEYWIYVEKPNVGYFASQKFRVQDIA
PSSPVEQLPPSPEQLKISTTTPMPSTCEASVSTVNGKSVACRNSIIFNEDFNLDNLRYWS
FDTRFPLDDATADAEFCIYEKRAETSFIRDGSMTLKAESLKKIAGFDDARIRIGSYNLKE
RCTPISNDERECSRQAQFGYILPPVTSAYLTTRSKFSFMYGRVEARLRAPIGDYLYAQIT
LQPQLKPEEAANDSSTSQHLKVFFARGNEQLKDADEEVGGSRVYGGAILSKNPKNNLKWL
KSKQFPNTHLGNDFHIYELLWTPTEISLSIDGIKYGSLSSNLRDSAMVAKIKSAVNWANN
GPFDREHFLSINLGAGSVKNFYSINNTLVNGAEFEPKPWSDTDPRAERSFYMAHDKWYPT
WKKPSLEVDYIKIYSV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9237.t1 | Coils | Coil | Coil | 736 | 736 | - |
| 7 | g9237.t1 | Gene3D | G3DSA:2.60.40.2140 | - | 20 | 123 | 6.5E-11 |
| 6 | g9237.t1 | Gene3D | G3DSA:2.60.40.2140 | - | 262 | 363 | 1.0E-8 |
| 3 | g9237.t1 | PANTHER | PTHR10963:SF43 | GRAM-NEGATIVE BACTERIA-BINDING PROTEIN 1-RELATED | 299 | 736 | 9.9E-68 |
| 4 | g9237.t1 | PANTHER | PTHR10963 | GLYCOSYL HYDROLASE-RELATED | 299 | 736 | 9.9E-68 |
| 1 | g9237.t1 | Pfam | PF15886 | Carbohydrate binding domain (family 32) | 23 | 107 | 5.0E-9 |
| 2 | g9237.t1 | Pfam | PF15886 | Carbohydrate binding domain (family 32) | 263 | 359 | 5.9E-7 |
| 10 | g9237.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 11 | g9237.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 12 | g9237.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 13 | g9237.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 20 | - |
| 9 | g9237.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 736 | - |
| 15 | g9237.t1 | ProSiteProfiles | PS51762 | Glycosyl hydrolases family 16 (GH16) domain profile. | 376 | 736 | 16.845 |
| 16 | g9237.t1 | ProSiteProfiles | PS50020 | WW/rsp5/WWP domain profile. | 693 | 726 | 8.532 |
| 5 | g9237.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 501 | 734 | 2.83E-27 |
| 14 | g9237.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 26 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0030246 | carbohydrate binding | MF |
| GO:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | MF |
| GO:0005515 | protein binding | MF |
| GO:0005975 | carbohydrate metabolic process | BP |
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