General information for g5994.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Maltase 2.
Parent gene
- The parent gene g5994 is located on chr_2: 13224141..13225689 (+ 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 | g5994 | g5994.t1 | TSS | g5994.t1 | 13223384 | 13223384 |
| chr_2 | g5994 | g5994.t1 | isoform | g5994.t1 | 13223433 | 13225689 |
| chr_2 | g5994 | g5994.t1 | exon | g5994.t1.exon1 | 13223433 | 13223912 |
| chr_2 | g5994 | g5994.t1 | cds | g5994.t1.CDS1 | 13223433 | 13223912 |
| chr_2 | g5994 | g5994.t1 | exon | g5994.t1.exon2 | 13223966 | 13224145 |
| chr_2 | g5994 | g5994.t1 | cds | g5994.t1.CDS2 | 13223966 | 13224145 |
| chr_2 | g5994 | g5994.t1 | exon | g5994.t1.exon3 | 13224216 | 13224323 |
| chr_2 | g5994 | g5994.t1 | cds | g5994.t1.CDS3 | 13224216 | 13224323 |
| chr_2 | g5994 | g5994.t1 | exon | g5994.t1.exon4 | 13224385 | 13224771 |
| chr_2 | g5994 | g5994.t1 | cds | g5994.t1.CDS4 | 13224385 | 13224771 |
| chr_2 | g5994 | g5994.t1 | exon | g5994.t1.exon5 | 13224830 | 13224895 |
| chr_2 | g5994 | g5994.t1 | cds | g5994.t1.CDS5 | 13224830 | 13224895 |
| chr_2 | g5994 | g5994.t1 | exon | g5994.t1.exon6 | 13224955 | 13225689 |
| chr_2 | g5994 | g5994.t1 | cds | g5994.t1.CDS6 | 13224955 | 13225689 |
| chr_2 | g5994 | g5994.t1 | TTS | g5994.t1 | 13225782 | 13225782 |
Sequences
>g5994.t1 Gene=g5994 Length=1956
ATGAAAGTGATTTTAGTGATTGTCTTATTTGCAAGTCTGACACTTGCACAAAAAGATTGG
TGGGAAACTGCTAATTTTTATCAAATTTATCCACGCAGTTTTAAAGATTCAGATAATGAT
GGTGTCGGTGATCTTCGTGGAATTATTGAAAATTTAGACTATTTGAAAGAACTTGGTGTT
ACTGCAACGTGGCTCAGTCCTATTTTGAAATCACCTCAAGTCGATTTTGGTTATGATATT
TCAGATTTTAGTGATGTGGATCCAATTTTTGGAACAATGGCTGATCTTGAAGAAATGTTT
GCAAAAGCTCATGATTTGGGTATAAAAGTTATTATGGATTTTGTACCAAACCATACTTCA
GACGAACATGAGTGGTTCAAGAAGTCAGTAGCAAGAGAAGGAAATTATACAGATTATTAT
GTGTGGCATAATGGTAAACCTAATCCTGAAGGTGGTCGAAATATTGAGCCAAATAATTGG
CAAGCAGTTTTCTCAACTCGTGCATGGTCATGGAACGAACAAAGACAGCAATATTATTTG
CATCAATTTGCAAGTGGTCAACCTGATTTGAATTTCCGAAATCCTCTTGTGGTTCAAGAA
ATGAAAAACGTTTTGACTTTTTGGCTCGAAAAGGGCGCAGACGGTTTTCGTATTGATGCG
ATAAACCACTTATTTGAAGTTGAAGACTTTAGAGACGAACCAGAAACTGGCTGGACAAAT
AACACAAACGATTATGGCTTTACTCACCATCATTACACTAAAGATTTGGATGAAACTTAT
GATATGGTTCGTGAATGGAGAAAATTAATTGATGATTTTAATGCCGCACATCCAGGAAAT
ACAAGAGTAATTTTCACAGAAGCTTATGCAAATGTATCATTCACAATGAAATACTATGGT
TCAGAAGCTGAACCTATTGCACACTTTCCTTTCAACTTTCTACTTATTGAAAAATTAAAT
GAAGGCTCGAATGCAAATGATTTTAAAAGAGAAATTGATGAATGGTTCACAAATTTGCCA
AATGCTCATGCGACATCAAACTGGGTTCTTGGAAATCATGACAAACCAAGATTTGCTTCA
CGTTATGGAACTGAAAGAGTTGATGGAATGTTGATGCTTTTGCTACTTCTTCCCGGAGTT
GCAGTAACCTATATGGGAGACGAAATTGGAATGGTTGATTTCCGTGATGGAATTTCTTGG
GAAGAGACTCTTGATCCACAAGCTTGCAACACAAGTCCAGAAGATTACAAATGGGCATCA
AGAGATCCAGTAAGAACGCCTTTCCAGTGGGACGCATCATATGCAGCTGGATTTTGTGCA
TCATGTAATAAAACATGGTTGCCACTCAATGACAATTACCAGACGTTAAATTTGGCAAAT
CAAAGAGCAGCTGAAAAGAGCTTCTTTAAATTCTATAAACAACTTTCGTCGCTTCGTACC
AATGAAGTTTTCGCAAATGGTGATTTTATGTCGCATGCATATGACGATGAAGTTTTTGCA
TACAAAAGAACATATAATGGTGAAACATTTGTGATTGTTATAAACTTTGGTGACAACAGG
CACACAATCAATGTTAATGACTTAAATGTGAGTTTCCCTGTACAATCAGAAGTTGTTGTT
GCTGGATCACTTTCAAGTTACGATGCTGGTGACTTAGTGCTATCGAATGCTTTGGTTTTA
ACAAGTCATGATGCAGTTGTTTTGAAAGCAAAAGCTACTGAAGATACAACGACTGTACAG
GCAACTACAACAGTATCATCAACAGTAACAAGTACTGATAATGAAGAGTCGACACCAACT
CCAACTCAACCAACTACAACAACGCAACCAACCACAACAACGCAACCAACCACAACAACG
CAACCAACAACCACAACTGATGGTGGTAGCTCAACAATAATTGCAAGTTTCTTTGCAATT
CTTTCACTTCTCTTCATAAATATCATTTTTAACTAA
>g5994.t1 Gene=g5994 Length=651
MKVILVIVLFASLTLAQKDWWETANFYQIYPRSFKDSDNDGVGDLRGIIENLDYLKELGV
TATWLSPILKSPQVDFGYDISDFSDVDPIFGTMADLEEMFAKAHDLGIKVIMDFVPNHTS
DEHEWFKKSVAREGNYTDYYVWHNGKPNPEGGRNIEPNNWQAVFSTRAWSWNEQRQQYYL
HQFASGQPDLNFRNPLVVQEMKNVLTFWLEKGADGFRIDAINHLFEVEDFRDEPETGWTN
NTNDYGFTHHHYTKDLDETYDMVREWRKLIDDFNAAHPGNTRVIFTEAYANVSFTMKYYG
SEAEPIAHFPFNFLLIEKLNEGSNANDFKREIDEWFTNLPNAHATSNWVLGNHDKPRFAS
RYGTERVDGMLMLLLLLPGVAVTYMGDEIGMVDFRDGISWEETLDPQACNTSPEDYKWAS
RDPVRTPFQWDASYAAGFCASCNKTWLPLNDNYQTLNLANQRAAEKSFFKFYKQLSSLRT
NEVFANGDFMSHAYDDEVFAYKRTYNGETFVIVINFGDNRHTINVNDLNVSFPVQSEVVV
AGSLSSYDAGDLVLSNALVLTSHDAVVLKAKATEDTTTVQATTTVSSTVTSTDNEESTPT
PTQPTTTTQPTTTTQPTTTTQPTTTTDGGSSTIIASFFAILSLLFINIIFN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g5994.t1 | CDD | cd11328 | AmyAc_maltase | 18 | 489 | 0.0 |
| 8 | g5994.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 20 | 480 | 1.2E-170 |
| 9 | g5994.t1 | Gene3D | G3DSA:3.90.400.10 | - | 120 | 194 | 1.2E-170 |
| 7 | g5994.t1 | Gene3D | G3DSA:2.60.40.1180 | - | 490 | 570 | 1.8E-7 |
| 20 | g5994.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 583 | 627 | - |
| 2 | g5994.t1 | PANTHER | PTHR10357 | ALPHA-AMYLASE FAMILY MEMBER | 15 | 578 | 5.4E-248 |
| 3 | g5994.t1 | PANTHER | PTHR10357:SF177 | FI17312P1-RELATED | 15 | 578 | 5.4E-248 |
| 1 | g5994.t1 | Pfam | PF00128 | Alpha amylase, catalytic domain | 43 | 395 | 1.4E-109 |
| 12 | g5994.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 13 | g5994.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 14 | g5994.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 11 | - |
| 16 | g5994.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 12 | 16 | - |
| 11 | g5994.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 631 | - |
| 15 | g5994.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 632 | 650 | - |
| 10 | g5994.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 651 | 651 | - |
| 19 | g5994.t1 | SMART | SM00642 | aamy | 28 | 425 | 7.0E-147 |
| 5 | g5994.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 18 | 481 | 1.11E-128 |
| 4 | g5994.t1 | SUPERFAMILY | SSF51011 | Glycosyl hydrolase domain | 487 | 539 | 4.27E-8 |
| 6 | g5994.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
| 18 | g5994.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 628 | 650 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5994/g5994.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5994.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 transcript has been annotated with K14210 (solute carrier family 3 (neutral and basic amino acid transporter), member 1)
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. There were no conditions that were differentially expressed