General information for g11892.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative TOX high mobility group box family member 3.
Parent gene
- The parent gene g11892 is located on chr_1: 19105383..19106286 (+ 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 | g11892 | g11892.t1 | isoform | g11892.t1 | 19091415 | 19106286 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon1 | 19091415 | 19092176 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS1 | 19091415 | 19092176 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon2 | 19096531 | 19096647 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS2 | 19096531 | 19096647 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon3 | 19100357 | 19100749 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS3 | 19100357 | 19100749 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon4 | 19102841 | 19102971 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS4 | 19102841 | 19102971 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon5 | 19103092 | 19103231 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS5 | 19103092 | 19103231 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon6 | 19105383 | 19106014 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS6 | 19105383 | 19106014 |
| chr_1 | g11892 | g11892.t1 | exon | g11892.t1.exon7 | 19106071 | 19106286 |
| chr_1 | g11892 | g11892.t1 | cds | g11892.t1.CDS7 | 19106071 | 19106286 |
| chr_1 | g11892 | g11892.t1 | TTS | g11892.t1 | 19106469 | 19106469 |
| chr_1 | g11892 | g11892.t1 | TSS | g11892.t1 | NA | NA |
Sequences
>g11892.t1 Gene=g11892 Length=2391
ATGAAATTTATCATTGTTAGTTTAATTGGAATTCCTGCAAGCGGAAAAAGCACACTTTCG
AGCATTATTTCAAAATTGTCAGCAGAATGCTTGCTAAATGCAAATGTGATAATTCTAAAT
TTTGACGATTTGATTGAAATTGATTATGGAAATATTTCTGATGGTGATTACAAAAAATCA
CGTGATTTTCTTTTTAATGAGATAGAAAAGTTGATAAAAATGTTGATGGATGAAAAAAAT
CCATTCAAATGGGCGCCAATAATTGAACAATCTGCTCTTAAAGTTCCATTGAATTTTATA
ACTATCAAAGAAGCAAATTCAAGCACGCTAATAATTCTTGACGACAATATGTATTATCGT
AGTATGAGACAACGAGCGAGACTCATTTCTAAGAATTGTCATTGTGAGCATTTTCAAATT
TTTGTCAAATCAGCATTATATGATGCGATTGAGAGAAACAAGAAACGAAAATCATCAGTT
GATGTTGGCGTAATTCAGAAAATGTTTAATGACATGGAAATTCCAATCAATGCGCGAACA
ATCAATGTTGATATTATGAATCTTAATGAAGAAACCTTTTTAAATGAGTTGAAAGATCGA
ATTAAAGAGCCAGAAGTATTAACAGAAGAACCACAAATGAAAGTTCCACAAGACCAATCA
ATTGTTCATGAAATAGATTTGATGACAAGAAAAGAAATTGGAATCGAAATTAAAAGAATT
GGAAACAAAGGAAATTTAAAGGAAATTTCAGAAAAATTAAATAGTAACGAAGAAAATTTG
AATGTTTCATTGTCCGTTCAAGGTCAGCAGCAGCAATTTAGTGGACAACAACAACACCAA
TCAATTGCAAATCAATATAGTGGAACAATGAGCGATCATACTTTTCATACGCCTTCATTT
GGTGACGAAGAATTTGATATTCCTGTTGATGTTTTGCATCATCCAACACAAGCACAACAG
CACAATCAATTAGATCAGTTTCAAATGCATGGTATGATAAATAATCAACATCAACAGGCA
TCACAGACATATGTTCAGCATCAACAATGGACACAACAACCATCAACAACAGAATTGACG
TATCAAAATCATTCCGATTATCATCACATGACGACAAATGCAAGCGAGAACATCCTAATG
ATGCCACAACAACAGCAACAGCAGCAGTTAATGAATACAAACACAAACAATTATGTGGAA
ACGCCAGCAAGTGCGCCAATTAGTAACAGTCACGAAAATGGTTCAACCAGCGATGATAGT
GACGATCCGAATAATACATTCAAGAATTTTGATGAGGATGGAAATGTCAAAGGAGAAATC
GAAGATACAAAGAAGATTATAGCAGTAAAAGCAAATACTGTTAAGGGAAAGAAGAAAAAA
AGAGATCCTAATGAACCCCTTAAACCTGTCTCAGCATATGCTCTGTTCTTTAGAGACACA
CAAGCGGCAATAAAAGGACAAAATCCCAATGCATCTTTTGGTGAAGTTTCAAAGATTGTC
GCTTCAATGTGGGACGTTTTAGCACCGGAACATAAAAATGTAATTAAAATGAAGAAAATT
TTTATTTTCTGTGTCGTGTGTACATTTTTATATTGCATAAATGCACAAACTCGTGTGAGA
AATCAACAAGGAGTTCAAAGAAAACAACCTCCAGCAAGAGTGTTAAATAAAGTTCAACCA
CCTGCAAATACTCGTACAAGAGCTCAACAGCAAGCTATAAGATTGCAAGCTCTGAACAAG
CAACGTGGTATTATGCCAAAAATCAATAAAGGACACAAAAGAATCAAGCCAGCATCAGTT
CGTGGATATTGGGATTCTAGTTTATGTATTGAAGATCCTGAAGGAGTATTTATTCATGAT
GATTGTGACAAATATTGGTATTGTCAGGATGGTGAAATATATGAATACTGGTGTCCAGAC
GATTTACCTATTTTTGACTCTGTGTTATTACAATGTGCACCAGAAGAATGGGGATGGTGT
GCAGCGTGGGGTGACAATAATTGGGATGCAGAATGTCCAGAAGATCCAAATGAATTAGGT
TTTATTCAAGGTGATACATGTGAAGATTATTACATTTGTATCAATGGATGGCCTGTTCAA
TGGTGGTGTGCTCCTGGACAGCATTTTAATATTAATGAATGGCATTGTGACATTCCATCA
TTAGCTGGATGTGATCCTAATGCTGTTGGACCAATGCCAGGTTTACCCGATTGCACTCAA
GATGGAATTCTTCCTCATCCTTATGATTGCAGTATGTTTATTTATTGTCAAAGGAATGGA
AATCGATTGATCCAAAAATGTCCTCATTTAGAAGAATTTAATCCTTCATTAGGGCGTTGT
TTAGTTCAATCACCAAGTGCTTGTTTTAATCAAAGCTTTATTCGCGGTTAA
>g11892.t1 Gene=g11892 Length=796
MKFIIVSLIGIPASGKSTLSSIISKLSAECLLNANVIILNFDDLIEIDYGNISDGDYKKS
RDFLFNEIEKLIKMLMDEKNPFKWAPIIEQSALKVPLNFITIKEANSSTLIILDDNMYYR
SMRQRARLISKNCHCEHFQIFVKSALYDAIERNKKRKSSVDVGVIQKMFNDMEIPINART
INVDIMNLNEETFLNELKDRIKEPEVLTEEPQMKVPQDQSIVHEIDLMTRKEIGIEIKRI
GNKGNLKEISEKLNSNEENLNVSLSVQGQQQQFSGQQQHQSIANQYSGTMSDHTFHTPSF
GDEEFDIPVDVLHHPTQAQQHNQLDQFQMHGMINNQHQQASQTYVQHQQWTQQPSTTELT
YQNHSDYHHMTTNASENILMMPQQQQQQQLMNTNTNNYVETPASAPISNSHENGSTSDDS
DDPNNTFKNFDEDGNVKGEIEDTKKIIAVKANTVKGKKKKRDPNEPLKPVSAYALFFRDT
QAAIKGQNPNASFGEVSKIVASMWDVLAPEHKNVIKMKKIFIFCVVCTFLYCINAQTRVR
NQQGVQRKQPPARVLNKVQPPANTRTRAQQQAIRLQALNKQRGIMPKINKGHKRIKPASV
RGYWDSSLCIEDPEGVFIHDDCDKYWYCQDGEIYEYWCPDDLPIFDSVLLQCAPEEWGWC
AAWGDNNWDAECPEDPNELGFIQGDTCEDYYICINGWPVQWWCAPGQHFNINEWHCDIPS
LAGCDPNAVGPMPGLPDCTQDGILPHPYDCSMFIYCQRNGNRLIQKCPHLEEFNPSLGRC
LVQSPSACFNQSFIRG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g11892.t1 | CDD | cd00009 | AAA | 8 | 78 | 6.04417E-4 |
| 22 | g11892.t1 | CDD | cd00084 | HMG-box | 466 | 514 | 6.00837E-13 |
| 13 | g11892.t1 | Gene3D | G3DSA:1.10.30.10 | DNA Binding (I) | 450 | 519 | 1.2E-20 |
| 12 | g11892.t1 | Gene3D | G3DSA:2.170.140.10 | Antimicrobial Protein | 667 | 729 | 2.4E-8 |
| 11 | g11892.t1 | Gene3D | G3DSA:2.170.140.10 | Antimicrobial Protein | 732 | 793 | 4.9E-7 |
| 26 | g11892.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 406 | 435 | - |
| 27 | g11892.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 406 | 423 | - |
| 5 | g11892.t1 | PANTHER | PTHR45781 | AGAP000281-PA | 269 | 518 | 1.2E-43 |
| 4 | g11892.t1 | Pfam | PF00505 | HMG (high mobility group) box | 467 | 512 | 4.3E-9 |
| 3 | g11892.t1 | Pfam | PF01607 | Chitin binding Peritrophin-A domain | 609 | 655 | 1.0E-6 |
| 2 | g11892.t1 | Pfam | PF01607 | Chitin binding Peritrophin-A domain | 678 | 724 | 3.2E-6 |
| 1 | g11892.t1 | Pfam | PF01607 | Chitin binding Peritrophin-A domain | 738 | 788 | 7.4E-8 |
| 16 | g11892.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 15 | - |
| 17 | g11892.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 18 | g11892.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 20 | g11892.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 15 | - |
| 15 | g11892.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 16 | 519 | - |
| 19 | g11892.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 520 | 539 | - |
| 14 | g11892.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 540 | 796 | - |
| 31 | g11892.t1 | ProSiteProfiles | PS50118 | HMG boxes A and B DNA-binding domains profile. | 466 | 512 | 10.894 |
| 28 | g11892.t1 | ProSiteProfiles | PS50940 | Chitin-binding type-2 domain profile. | 606 | 662 | 9.334 |
| 30 | g11892.t1 | ProSiteProfiles | PS50940 | Chitin-binding type-2 domain profile. | 669 | 726 | 11.909 |
| 29 | g11892.t1 | ProSiteProfiles | PS50940 | Chitin-binding type-2 domain profile. | 735 | 790 | 10.792 |
| 23 | g11892.t1 | SMART | SM00494 | chi_10 | 607 | 662 | 1.7 |
| 25 | g11892.t1 | SMART | SM00494 | chi_10 | 670 | 726 | 2.0E-6 |
| 24 | g11892.t1 | SMART | SM00494 | chi_10 | 736 | 790 | 6.8E-8 |
| 6 | g11892.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 5 | 203 | 9.76E-13 |
| 7 | g11892.t1 | SUPERFAMILY | SSF47095 | HMG-box | 454 | 513 | 2.62E-14 |
| 10 | g11892.t1 | SUPERFAMILY | SSF57625 | Invertebrate chitin-binding proteins | 606 | 661 | 5.75E-7 |
| 9 | g11892.t1 | SUPERFAMILY | SSF57625 | Invertebrate chitin-binding proteins | 672 | 729 | 5.49E-10 |
| 8 | g11892.t1 | SUPERFAMILY | SSF57625 | Invertebrate chitin-binding proteins | 733 | 789 | 2.62E-11 |
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:0008061 | chitin binding | MF |
| GO:0005576 | extracellular region | CC |
KEGG
Orthology
- This transcript has been annotated with K10837 (O-phosphoseryl-tRNA(Sec) kinase)
Pathway
- This transcript belongs to the following pathways
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.
