General information for g11881.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Alpha-L-iduronidase.
Parent gene
- The parent gene g11881 is located on chr_1: 18955185..18961632 (+ 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 | g11881 | g11881.t3 | TSS | g11881.t3 | 18953099 | 18953099 |
| chr_1 | g11881 | g11881.t3 | isoform | g11881.t3 | 18953101 | 18954571 |
| chr_1 | g11881 | g11881.t3 | exon | g11881.t3.exon1 | 18953101 | 18953381 |
| chr_1 | g11881 | g11881.t3 | cds | g11881.t3.CDS1 | 18953104 | 18953381 |
| chr_1 | g11881 | g11881.t3 | exon | g11881.t3.exon2 | 18953433 | 18953614 |
| chr_1 | g11881 | g11881.t3 | cds | g11881.t3.CDS2 | 18953433 | 18953614 |
| chr_1 | g11881 | g11881.t3 | exon | g11881.t3.exon3 | 18953676 | 18953771 |
| chr_1 | g11881 | g11881.t3 | cds | g11881.t3.CDS3 | 18953676 | 18953771 |
| chr_1 | g11881 | g11881.t3 | exon | g11881.t3.exon4 | 18953833 | 18954571 |
| chr_1 | g11881 | g11881.t3 | cds | g11881.t3.CDS4 | 18953833 | 18954569 |
| chr_1 | g11881 | g11881.t3 | TTS | g11881.t3 | 18955289 | 18955289 |
Sequences
>g11881.t3 Gene=g11881 Length=1298
AAAATGAAAAAAATTTTGGTATTTTTTTATTGCCTGATTTTCATTTACCTCGTATATGGT
CGAGTTAATGTAATTGATTATGAAAAATCAACAAATGTTATGAAAAGAATGCCAAAATTT
TGGACAAATACTGGCTTTGCCCCAACTGAACCAATCAACAATGTTTTCGATTTCTTTGAG
ACAAAAGATTTAAATATGAATTTAGAAATCATTGGATCAATGCCCAATAATGGACTAAAA
TACATTCGAATACATTGGCTTTTGAATTTAATAAAAATTAGTGGATATGACAGCAAAAAT
CAACCAATATTTAATTTTGAAAAATTAGATACTTTTTTAAGAAAAATGATTAATGAATAT
AACTTATTGCCTGTAATTGAATTTATGACAACTTTAAAGTTTAAAAATATGAACAAAGAT
TCATGGAAAACACTTTCTTATCAAATTATTACACATTATGCAGAAATTTATGGATTAAAA
AATGTTGCAAAATGGAAATTTGAATCCTGGAATGAACCTGATCTTAAAAATTATAACAAA
CTCAACTTTACTTTATCAGATTATTTGGAATACATTTATGGTATAAAAGAAGGTTTAGAA
TTAGCTGAGAGAAATTTCACCTCAAAATATATTTTAAAACTAAGAGGACCAGCTGGATTA
TTCAAAGATGAAAAGAATCATAAATTTTGTTGGTCTGTATTAGAAAAATGTAATCAGAAT
ATTACAAATTGCCCAATTGATATAATAACATTTCATCGAAAAGGAAATGGAATCGAAGCT
AATGAAATAATTGATACAAGTTTTACATTAATAGATGAATTTTCTACAAGATTTAAAAAT
CTTTCAAAATTTAAATATTCTAATACTGAAGCAGATCCAATAAAAACTTGGTCACAACCT
CGTGATTTTCAGTCAGATACAAGGTATGCTTCTATTTTAGTAGAAACAATATTTCAGTAT
TGGAAAGCAAAATTTGAAAAACAAATGACAAATTTGGAGTCAATTAGTCATGATAATAGT
TTTATGAATTTTTATCCAAATATTTTCACACAACGGACATTATTGGCAAGATTTCAAATG
AATAACAGTGTACCAATATATAGTCAAATTATTCAAAAACCTGTATACAGTGCATTGGGA
TTGATTGCAAATTTAGCTAAAAATGCATCAAATTATCAGAAAACACAAAACCTTTCTTAT
CTCATAACGACACATAATGGAAGAAAAAATAATAAATTTTACTCATGTATAATTATTTTA
ACGCATGTAAACACAACAAAAAATAATAACAGAACAAA
>g11881.t3 Gene=g11881 Length=431
MKKILVFFYCLIFIYLVYGRVNVIDYEKSTNVMKRMPKFWTNTGFAPTEPINNVFDFFET
KDLNMNLEIIGSMPNNGLKYIRIHWLLNLIKISGYDSKNQPIFNFEKLDTFLRKMINEYN
LLPVIEFMTTLKFKNMNKDSWKTLSYQIITHYAEIYGLKNVAKWKFESWNEPDLKNYNKL
NFTLSDYLEYIYGIKEGLELAERNFTSKYILKLRGPAGLFKDEKNHKFCWSVLEKCNQNI
TNCPIDIITFHRKGNGIEANEIIDTSFTLIDEFSTRFKNLSKFKYSNTEADPIKTWSQPR
DFQSDTRYASILVETIFQYWKAKFEKQMTNLESISHDNSFMNFYPNIFTQRTLLARFQMN
NSVPIYSQIIQKPVYSALGLIANLAKNASNYQKTQNLSYLITTHNGRKNNKFYSCIIILT
HVNTTKNNNRT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11881.t3 | Gene3D | G3DSA:2.60.40.1500 | Glycosyl hydrolase domain; family 39 | 34 | 429 | 1.4E-126 |
| 10 | g11881.t3 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 37 | 385 | 1.4E-126 |
| 2 | g11881.t3 | PANTHER | PTHR12631:SF8 | ALPHA-L-IDURONIDASE | 31 | 389 | 3.1E-62 |
| 3 | g11881.t3 | PANTHER | PTHR12631 | ALPHA-L-IDURONIDASE | 31 | 389 | 3.1E-62 |
| 6 | g11881.t3 | PRINTS | PR00745 | Glycosyl hydrolase family 39 signature | 144 | 161 | 9.3E-7 |
| 4 | g11881.t3 | PRINTS | PR00745 | Glycosyl hydrolase family 39 signature | 161 | 177 | 9.3E-7 |
| 5 | g11881.t3 | PRINTS | PR00745 | Glycosyl hydrolase family 39 signature | 301 | 318 | 9.3E-7 |
| 1 | g11881.t3 | Pfam | PF01229 | Glycosyl hydrolases family 39 | 32 | 429 | 8.1E-43 |
| 12 | g11881.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 13 | g11881.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g11881.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 15 | g11881.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 11 | g11881.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 431 | - |
| 17 | g11881.t3 | ProSitePatterns | PS01027 | Glycosyl hydrolases family 39 active site. | 164 | 173 | - |
| 7 | g11881.t3 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 39 | 384 | 3.16E-29 |
| 8 | g11881.t3 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 16 | g11881.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 5 | 24 | - |
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:0004553 | hydrolase activity, hydrolyzing O-glycosyl compounds | 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