General information for g1644.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lysosomal acid glucosylceramidase.
Parent gene
- The parent gene g1644 is located on chr_3: 12275318..12276322 (- 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_3 | g1644 | g1644.t6 | TTS | g1644.t6 | 12274247 | 12274247 |
| chr_3 | g1644 | g1644.t6 | isoform | g1644.t6 | 12274348 | 12276322 |
| chr_3 | g1644 | g1644.t6 | exon | g1644.t6.exon1 | 12274348 | 12274447 |
| chr_3 | g1644 | g1644.t6 | exon | g1644.t6.exon2 | 12274520 | 12274713 |
| chr_3 | g1644 | g1644.t6 | cds | g1644.t6.CDS1 | 12274712 | 12274713 |
| chr_3 | g1644 | g1644.t6 | exon | g1644.t6.exon3 | 12274764 | 12274922 |
| chr_3 | g1644 | g1644.t6 | cds | g1644.t6.CDS2 | 12274764 | 12274922 |
| chr_3 | g1644 | g1644.t6 | exon | g1644.t6.exon4 | 12274980 | 12275771 |
| chr_3 | g1644 | g1644.t6 | cds | g1644.t6.CDS3 | 12274980 | 12275771 |
| chr_3 | g1644 | g1644.t6 | exon | g1644.t6.exon5 | 12275860 | 12276216 |
| chr_3 | g1644 | g1644.t6 | cds | g1644.t6.CDS4 | 12275860 | 12276216 |
| chr_3 | g1644 | g1644.t6 | exon | g1644.t6.exon6 | 12276271 | 12276322 |
| chr_3 | g1644 | g1644.t6 | cds | g1644.t6.CDS5 | 12276271 | 12276322 |
| chr_3 | g1644 | g1644.t6 | TSS | g1644.t6 | 12276371 | 12276371 |
Sequences
>g1644.t6 Gene=g1644 Length=1654
ATGCATAATATGATACTAAAATTTTTGTCGATTTTTGCAACTTTATCATTAACAACTGCA
ACTTCTTTACCATGCATATTAAAATCATTTAACACTGGTTTAGTTTGTGTTTGCAATTCA
ACATATTGCGATAATTTAATAATAAATCTACCAGTAAAACGAAGTGAAGTTCATATATTT
TCTACATCTAAAAGTGGTCTTCGTTTTCATGAAGCAAAATCAAAATTTAATAATGAAAAA
ATTAAAATTCCTAATGGAGCTTTTCATTATGGCTCAGATATGCCACCTTATTATAAACGA
TTCATGCAAGTTGTTCAAAAAGTTGAAGGAATTGATGAACCAGTTGATTCAGTTGTGAAT
GTAGAAATCAATCGAACTGCACACTTTCAAAAAATTTTGGGTTTTGGGGGCGCATTTACT
GGAGCAGTGTCATACAATTTGAAGTTATTAAGTAAAGAATTGCAGGAACATGTCTATAAA
GCTTATTATTCAAAAGACATTGGCATTGGCTATAATTTAATGAGAATTCCCATTGGTGGT
TGTGATTTTGACCTCGCATCATGGACATATAATGAGAAACCCGAGCATGATCCTTATTTA
AGTAATTTTACACATCTTGATGAACGTGATTTGGATAAAATCAAACAAATTAATGAGTTA
AAAAAAATCACAAAAAATAATGATATAAAAATTTTTGGAGCTGCTTGGAGTCCACCTATT
TGGATGAAAACAAACAACGAATATACAGGTTTAAGTGCATTGAGAGAAGAATATTATCAA
ACTTGGGCAGACTATCATGTCAAATATCTTGAACTGATGGCCAAAAATAATCTACCGTTT
TGGGCAATTTCAACAGGCAATGAACCGCTGAATGGGATTCTTTTTCCTTACTTTGTTCAT
TTTATGTCACTCGGATGGGATCCTGCTATGCAGGGAAAATGGTTAGGGGAGAATTTAGGT
CCAGCAATGAAAAATTCTACATTCACAAAAAACATTTTAATCCTCGGTGGAGATGATCAA
CGTTATACATTACCTATATGGTTTCAACAAATGTTTAAAAGCAATGGTGATTCATGTGAC
TATCTTGATGGATTTGCAGTTCATTGGTATGCTGATAAATTTGTTCCTGCTAAAATGCTT
GATGACACAGCTACATTGTTCCCTGATAAATTTATAATTGCAACAGAAGCATCATCGGGA
GATCGTCCATGGGATATGCATAAGCCAGTCTTAGGATCATGGAGTAGATTTGAAGATTAT
ACAATCGACATAATGGAAGATTTCAATCATTTCGTGAGTGCTTGGGTCGATTGGAATTTA
ATTTTGGATGAAGAAGGTGGACCAAATTATGCTAAAGTATAACACAGTTGATGCTGCTAT
GATTGCTACTGAAAATCAAATTTACAAACAGCCGATTTTTTATGCAATTGGACATTTCTC
AAAGTTTGTATTGCCAGGTTCAGTAAGAATCAAATCAAAACCGTCAAATCGCTTTATAAA
AAGCGTGTCATTTTTACGGCCCGATGGATATATTGTGGTAATTTTGTATAATATAGCTGA
ACATAGCATGGATGTAAACGTTTTTGATAAAGAGCATGGTGTTTTGCGATTGGAACTTCC
AGCAAAATCACTACACACATTGATTTATAAATAG
>g1644.t6 Gene=g1644 Length=453
MHNMILKFLSIFATLSLTTATSLPCILKSFNTGLVCVCNSTYCDNLIINLPVKRSEVHIF
STSKSGLRFHEAKSKFNNEKIKIPNGAFHYGSDMPPYYKRFMQVVQKVEGIDEPVDSVVN
VEINRTAHFQKILGFGGAFTGAVSYNLKLLSKELQEHVYKAYYSKDIGIGYNLMRIPIGG
CDFDLASWTYNEKPEHDPYLSNFTHLDERDLDKIKQINELKKITKNNDIKIFGAAWSPPI
WMKTNNEYTGLSALREEYYQTWADYHVKYLELMAKNNLPFWAISTGNEPLNGILFPYFVH
FMSLGWDPAMQGKWLGENLGPAMKNSTFTKNILILGGDDQRYTLPIWFQQMFKSNGDSCD
YLDGFAVHWYADKFVPAKMLDDTATLFPDKFIIATEASSGDRPWDMHKPVLGSWSRFEDY
TIDIMEDFNHFVSAWVDWNLILDEEGGPNYAKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g1644.t6 | Gene3D | G3DSA:3.20.20.80 | Glycosidases | 109 | 453 | 8.1E-103 |
| 2 | g1644.t6 | PANTHER | PTHR11069 | GLUCOSYLCERAMIDASE | 15 | 452 | 2.4E-126 |
| 3 | g1644.t6 | PANTHER | PTHR11069:SF23 | LYSOSOMAL ACID GLUCOSYLCERAMIDASE | 15 | 452 | 2.4E-126 |
| 1 | g1644.t6 | Pfam | PF02055 | Glycosyl hydrolase family 30 TIM-barrel domain | 132 | 451 | 3.3E-76 |
| 9 | g1644.t6 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 10 | g1644.t6 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 7 | - |
| 11 | g1644.t6 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 8 | 17 | - |
| 12 | g1644.t6 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 22 | - |
| 8 | g1644.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 453 | - |
| 4 | g1644.t6 | SUPERFAMILY | SSF51445 | (Trans)glycosidases | 132 | 451 | 8.72E-63 |
| 6 | g1644.t6 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 13 | g1644.t6 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 24 | - |
| 5 | g1644.t6 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 20 | - |
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:0006665 | sphingolipid metabolic process | BP |
| GO:0004348 | glucosylceramidase 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.
