General information for g13263.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lactase-phlorizin hydrolase.
Parent gene
- The parent gene g13263 is located on chr_1: 28852462..28858079 (- 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 | g13263 | g13263.t1 | TTS | g13263.t1 | 28851896 | 28851896 |
| chr_1 | g13263 | g13263.t1 | isoform | g13263.t1 | 28851947 | 28854470 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon1 | 28851947 | 28852408 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS1 | 28851947 | 28852408 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon2 | 28852462 | 28852862 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS2 | 28852462 | 28852862 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon3 | 28853017 | 28853164 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS3 | 28853017 | 28853164 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon4 | 28853242 | 28853420 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS4 | 28853242 | 28853420 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon5 | 28853492 | 28853633 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS5 | 28853492 | 28853633 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon6 | 28854062 | 28854191 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS6 | 28854062 | 28854191 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon7 | 28854276 | 28854341 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS7 | 28854276 | 28854341 |
| chr_1 | g13263 | g13263.t1 | exon | g13263.t1.exon8 | 28854412 | 28854470 |
| chr_1 | g13263 | g13263.t1 | cds | g13263.t1.CDS8 | 28854412 | 28854470 |
| chr_1 | g13263 | g13263.t1 | TSS | g13263.t1 | 28854580 | 28854580 |
Sequences
>g13263.t1 Gene=g13263 Length=1587
ATGAATAAGAGTGCTTCCTTGTGTAAATTTTTGTTGATAAGTTTATTATATTTATCTATA
TTTGTGCGATGTGAAAAATTTGAATCATTTCCTGATGAATTCAAATGGGGAGTTGGGACA
TCAAGCTATCAAATTGAAGGTTCATGGAATGTTGATGGAAAAAGTGAATCTATTTGGGAT
CATTTGACACACAATTTTCCTGAAAAAATTGAAGATCAAAGCAATGCTGATCATACTACA
GAAAGCTATAAATTTTGGAAGCGTGATGTTGAGATGGTTCGTGAACTGGGAGTTGGTGTT
TATCGTTTTTCAATATCATGGCCAAGAGTGTTACCGAATGGCTATAAAAATCACATTAAC
AGAGCAGGTTTAGACTATTACAATAACATCATCAATGAATTGTTGACTTACAACATTACA
CCATTTGTAACAATCTATCATTGGGAATTGCCACAAAGACTGCAAGAACTCGGAGGCTGG
ACAAATCCAGAATTGATTGATATTTTTATTGATTATGCAAAAGTCTTGTTTGACGAATTT
GGTGATCGTGTAAAAATGTGGACAACATTCAATGAGCCTTGGCATATTTGTGAACAAGCT
TATGGACAAGATTATATGGCACCTTCTTACGATTATCCAGGTATTCCGATATACCTCTGT
GGTCACAATTTATTGAAAGCACATGCGAAAGTTTATCATATGTACAAAAACATATATAAT
CATGGTATTATTGGAATTACAGCAGACATTAGCACACCTCATCCACTAAATCACAATCAT
CATCATGATCAACAAGCAGTAGAACGAGCATATCAATTTTATCTCGGATGGTTTATGCAT
CCTATTTTCTCTAAGCATGGGAATTATCCAAAAATTATGATTGATCGAATTGGTGAATTA
AGTAAGAAGCAAGGATTTACAAAATCTCGTCTACCAACATTTACTAATGATGAAATAAAA
ATGATTCATAAAACATCGGATTTCTTCGGTATCAATAGCTACACATCAATTCAAGTGACA
TTAAATGATGATGACACAAATCCTGCTAAGCATAAAATCCCTTCCTTTTTTCATGATATG
GGAACAATAGAGTCACAAAATGAAAATTGGGAGAAAAGTGGAAGTGTGTGGTTGAGAGTG
CATCCAAGTGGAATGCTTCATTTATTAAAGTGGATCAAAAAAGAATATCACAATCCACCA
GTATATATTACTGAAAATGGTGTTAGCGATAAAGGTGGACTTAACGATGTAAAGCGTGTA
GAGTATTTCAATTCCTACTTGACGGCAATTTTAAATGCAATAAATGATGGATGTGATGTT
CGTGGTTATATTGCTTGGTCTTTAATGGATTCTTATGAATGGAAAGCTGGTTTCACCGAG
AAATTTGGTCTCTACCATGTTGATTTTAATTCACCTAATAAAACTCGCACACCTAAGATG
TCTGCAAAGGTCTTTAGTGAAATTGTAAAGACAAACAAAATTGATTGGTCATATTTGCCA
TTAATTGATGAAAAATCATCAAGTTATAATATTAAGCAATCAGCTTTTGTATTGGTTTTT
GCTTCAATAATTTTATCGTCATTATAA
>g13263.t1 Gene=g13263 Length=528
MNKSASLCKFLLISLLYLSIFVRCEKFESFPDEFKWGVGTSSYQIEGSWNVDGKSESIWD
HLTHNFPEKIEDQSNADHTTESYKFWKRDVEMVRELGVGVYRFSISWPRVLPNGYKNHIN
RAGLDYYNNIINELLTYNITPFVTIYHWELPQRLQELGGWTNPELIDIFIDYAKVLFDEF
GDRVKMWTTFNEPWHICEQAYGQDYMAPSYDYPGIPIYLCGHNLLKAHAKVYHMYKNIYN
HGIIGITADISTPHPLNHNHHHDQQAVERAYQFYLGWFMHPIFSKHGNYPKIMIDRIGEL
SKKQGFTKSRLPTFTNDEIKMIHKTSDFFGINSYTSIQVTLNDDDTNPAKHKIPSFFHDM
GTIESQNENWEKSGSVWLRVHPSGMLHLLKWIKKEYHNPPVYITENGVSDKGGLNDVKRV
EYFNSYLTAILNAINDGCDVRGYIAWSLMDSYEWKAGFTEKFGLYHVDFNSPNKTRTPKM
SAKVFSEIVKTNKIDWSYLPLIDEKSSSYNIKQSAFVLVFASIILSSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g13263.t1 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 21 | 500 | 6.1E-187 |
| 2 | g13263.t1 | PANTHER | PTHR10353:SF36 | CYTOSOLIC BETA-GLUCOSIDASE | 23 | 498 | 1.7E-169 |
| 3 | g13263.t1 | PANTHER | PTHR10353 | GLYCOSYL HYDROLASE | 23 | 498 | 1.7E-169 |
| 6 | g13263.t1 | PRINTS | PR00131 | Glycosyl hydrolase family 1 signature | 325 | 339 | 8.8E-19 |
| 4 | g13263.t1 | PRINTS | PR00131 | Glycosyl hydrolase family 1 signature | 401 | 409 | 8.8E-19 |
| 5 | g13263.t1 | PRINTS | PR00131 | Glycosyl hydrolase family 1 signature | 416 | 427 | 8.8E-19 |
| 8 | g13263.t1 | PRINTS | PR00131 | Glycosyl hydrolase family 1 signature | 437 | 454 | 8.8E-19 |
| 7 | g13263.t1 | PRINTS | PR00131 | Glycosyl hydrolase family 1 signature | 461 | 473 | 8.8E-19 |
| 1 | g13263.t1 | Pfam | PF00232 | Glycosyl hydrolase family 1 | 28 | 493 | 3.8E-151 |
| 13 | g13263.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 24 | - |
| 14 | g13263.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 15 | g13263.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 20 | - |
| 16 | g13263.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 21 | 24 | - |
| 12 | g13263.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 25 | 528 | - |
| 18 | g13263.t1 | ProSitePatterns | PS00653 | Glycosyl hydrolases family 1 N-terminal signature. | 34 | 48 | - |
| 17 | g13263.t1 | ProSitePatterns | PS00572 | Glycosyl hydrolases family 1 active site. | 401 | 409 | - |
| 9 | g13263.t1 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 29 | 492 | 4.53E-158 |
| 10 | g13263.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 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.
