General information for g5993.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Maltase 2.
Parent gene
- The parent gene g5993 is located on chr_2: 13219931..13220650 (+ 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 | g5993 | g5993.t1 | TSS | g5993.t1 | 13218283 | 13218283 |
| chr_2 | g5993 | g5993.t1 | isoform | g5993.t1 | 13218299 | 13220650 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon1 | 13218299 | 13218539 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS1 | 13218299 | 13218539 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon2 | 13218599 | 13218756 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS2 | 13218599 | 13218756 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon3 | 13218819 | 13218959 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS3 | 13218819 | 13218959 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon4 | 13219068 | 13219361 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS4 | 13219068 | 13219361 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon5 | 13219431 | 13219507 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS5 | 13219431 | 13219507 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon6 | 13219570 | 13219862 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS6 | 13219570 | 13219862 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon7 | 13219923 | 13220071 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS7 | 13219923 | 13220071 |
| chr_2 | g5993 | g5993.t1 | exon | g5993.t1.exon8 | 13220129 | 13220650 |
| chr_2 | g5993 | g5993.t1 | cds | g5993.t1.CDS8 | 13220129 | 13220650 |
| chr_2 | g5993 | g5993.t1 | TTS | g5993.t1 | 13220720 | 13220720 |
Sequences
>g5993.t1 Gene=g5993 Length=1875
ATGAAGTGGTTAGTATTAATAAATTTACTAATAGCAGTGATAACTGTAAAAGCAGGCTGG
CTGCCATTTTGGGTAGATGAAGAAGTAGAAGTTGAACTTTCTAACGAATTTGATTGGTGG
GAAAATGGAGTATTTTATCAAATTTATCCAAGATCATTTAAAGATGACAATAATGATGGA
ACTGGTGATATCAAGGGAATTATTTCGAAACTTGAACACTTGAAAGATTTGGGAGTAACA
GGAACTTGGCTTAGTCCAATTTTTAAAAGTCCTATGGTCGATGGAGGCTACGATATTTCA
GATTATACTGATGTCAATGAAATTTATGGAACTAAAGAAGATTTAAAAGCATTATTTGAT
AAAGCAAAAGAACTTGGACTTAAAATTATTCTTGACTTTGTGCCAAATCACTCAAGTGAT
CAACACGAGTGGTTCCAAAAATCAGTAAATAATGTTTCAGAATATGCAAATTATTATACA
TGGCGTGAATGTGAATTAGTTAATGCAACAACTGGTGAAAGAAGATTAGTTAATAATTGG
ATTGCCGTGTTCAATACACCAATGTGGACTTACAATGCACAACGTAACATGTGTTATCAT
CATCAATTTACTCCCGAACAACCTGATATGAATTACAGGCATCCAGATAAAGTAATTCAA
AAAGAAATGTTCAACATTTTAGACTATTGGATGGATCAGGGTGCAGATGGTTTCCGAGTC
GATGCTATCAATCATCTTTTTGAATCAGCTTCATTCACAAATCAACCACTTCTTTCTCCT
GACCTTGATCCGACACTCTACAGCAGTTATAACCCTCTCTACACTAGAGACTTGCCCGAG
TCGTATCAATTCATTTATGATGTGCGCGAGCATATGGATGAATACTCGAGAAATCATGGC
AATGTTACAAGGATTCTTATGACAGAAGCTTATGCGTCAGTTAAACAACAAACTTCCTGG
TATGGTTCATATGCACGTCCTGGTTCACACGTACCATTCAACTTTGTTTTCATCGCTGAT
ATTACGGCAGAATCGAATGCTACACATTATAAGGGCCTTGTTGATGAATGGATGGAAAAT
ACTCCATCATTTGCAATGGGTCAAGCAAATTGGGTGCTCGGAAATCACGACAGACCAAGA
CTTCGTTCAAGATTTGGTGAGGAACGTTTTGAAAGCATGGCTGTTATGTATATGATGTTG
CCAGGATTAGCAATTGTTTATTATGGTGAAGAAATTGGAATGATAGATAATTATAACATA
ACTTGGGAACAAACAGATGATCCACAAGCTTGCCAATCAAATTCATCAGTTTATATGCAA
TTTTCAAGAGATCCAGTTAGAACACCAATGCAGTGGGATGATTCACAATTTACTGGATTT
TGTGAAAATTGTGAACCTTGGCTACCAATACATGCAAACTATAGTCAAATTAATGTAAAG
AATCAAATTAATGATGAAAAGAGTACACTTAGTTTATATAAGAATCTGATTGCATTGCGT
AAAGAAAAAGAAGTGTTGAAAAAAGGCGGAATAACAACACAAACACTTGCTGGTGATGAA
GTGTTTGCATTTAAACGAACCATGAACAATGAGCCGACCATTGCTGTTTTCCTTAATCTT
GCATCTACGGAAAAGACAGTTAGCCTTAGAGATTTACTTCATGCTGATGATATTACAAGT
AAAACTAAAGCAACAGTGTTGATTGCAAACAACAAAGCAAGTCTTTCAAAAGGTGATTTT
TTTTCGGATATTAATAGTATCACTCTTGGAGGATATGACGCTGTTGTTTTTGAGATTTCA
TCTGCGACACGTATAGCCAAAGGTGCTGCGTTTACAATCACAATCTTCTGGATTATCGTG
AAGATTTTTGTGTAA
>g5993.t1 Gene=g5993 Length=624
MKWLVLINLLIAVITVKAGWLPFWVDEEVEVELSNEFDWWENGVFYQIYPRSFKDDNNDG
TGDIKGIISKLEHLKDLGVTGTWLSPIFKSPMVDGGYDISDYTDVNEIYGTKEDLKALFD
KAKELGLKIILDFVPNHSSDQHEWFQKSVNNVSEYANYYTWRECELVNATTGERRLVNNW
IAVFNTPMWTYNAQRNMCYHHQFTPEQPDMNYRHPDKVIQKEMFNILDYWMDQGADGFRV
DAINHLFESASFTNQPLLSPDLDPTLYSSYNPLYTRDLPESYQFIYDVREHMDEYSRNHG
NVTRILMTEAYASVKQQTSWYGSYARPGSHVPFNFVFIADITAESNATHYKGLVDEWMEN
TPSFAMGQANWVLGNHDRPRLRSRFGEERFESMAVMYMMLPGLAIVYYGEEIGMIDNYNI
TWEQTDDPQACQSNSSVYMQFSRDPVRTPMQWDDSQFTGFCENCEPWLPIHANYSQINVK
NQINDEKSTLSLYKNLIALRKEKEVLKKGGITTQTLAGDEVFAFKRTMNNEPTIAVFLNL
ASTEKTVSLRDLLHADDITSKTKATVLIANNKASLSKGDFFSDINSITLGGYDAVVFEIS
SATRIAKGAAFTITIFWIIVKIFV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5993.t1 | CDD | cd11328 | AmyAc_maltase | 36 | 510 | 0.0 |
| 7 | g5993.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 39 | 501 | 8.3E-154 |
| 8 | g5993.t1 | Gene3D | G3DSA:3.90.400.10 | - | 139 | 214 | 8.3E-154 |
| 6 | g5993.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 516 | 599 | 2.9E-7 |
| 2 | g5993.t1 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 32 | 606 | 1.1E-202 |
| 3 | g5993.t1 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 32 | 606 | 1.1E-202 |
| 1 | g5993.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 62 | 417 | 1.8E-88 |
| 10 | g5993.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 11 | g5993.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 12 | g5993.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 13 | g5993.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 9 | g5993.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 624 | - |
| 15 | g5993.t1 | SMART | SM00642 | aamy | 47 | 447 | 5.1E-115 |
| 4 | g5993.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 37 | 506 | 7.38E-120 |
| 5 | g5993.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5993/g5993.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5993.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005975 | carbohydrate metabolic process | BP |
| GO:0003824 | catalytic activity | MF |
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