General information for g4935.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Mannosyl-oligosaccharide glucosidase GCS1.
Parent gene
- The parent gene g4935 is located on chr_2: 6090384..6091438 (- 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 | g4935 | g4935.t1 | TTS | g4935.t1 | 6088556 | 6088556 |
| chr_2 | g4935 | g4935.t1 | isoform | g4935.t1 | 6088698 | 6091438 |
| chr_2 | g4935 | g4935.t1 | exon | g4935.t1.exon1 | 6088698 | 6090308 |
| chr_2 | g4935 | g4935.t1 | cds | g4935.t1.CDS1 | 6088698 | 6090308 |
| chr_2 | g4935 | g4935.t1 | exon | g4935.t1.exon2 | 6090383 | 6091060 |
| chr_2 | g4935 | g4935.t1 | cds | g4935.t1.CDS2 | 6090383 | 6091060 |
| chr_2 | g4935 | g4935.t1 | exon | g4935.t1.exon3 | 6091119 | 6091361 |
| chr_2 | g4935 | g4935.t1 | cds | g4935.t1.CDS3 | 6091119 | 6091361 |
| chr_2 | g4935 | g4935.t1 | exon | g4935.t1.exon4 | 6091436 | 6091438 |
| chr_2 | g4935 | g4935.t1 | cds | g4935.t1.CDS4 | 6091436 | 6091438 |
| chr_2 | g4935 | g4935.t1 | TSS | g4935.t1 | 6091494 | 6091494 |
Sequences
>g4935.t1 Gene=g4935 Length=2535
ATGGTGAGAAATCGAAAACAGCATCAGCAAAATGAAAATTCGTCCAAACAAAAATCCACA
TCTTCAAAAAATGAAGAGAAGGCCAGCAGTAGTAATAGCAATTCAACAAGCTCAACAACT
ACGACACACAATAGTAATTCAAGTCCTACATTCTCTTCATCTAGAAAGATGATTCCATCA
TGGTATATTTCAATCGGTGTAGCCAGTATTGCTGTTGTCATGTATTTTGTTTATCAGGGA
TATTTGGAAACTCGAGTAAACACACCGCTAGATGAAAAAAGAATTGTTCCGAAACAACCA
GACTCGGAGAAGTTCTGGAACACTTATCGTGCAAACACATATTTCGGTTTAAAAACTCGC
GATCCAAACTCAATGGTGCTTGGTTTGATGTGGTATTTTCCAAATAAACTACGACCAAAT
GGTGATGGCATAAGACATTGGTGTAAATTAGAAGATAATCTTAAAAAGTATGGCTGGTTG
CAGCACGATGGCAAAAATTTTGGTATACAAGAAATTCATGAAGATAATTACGTACTTGAA
ACTTCATTCATCAAGTTTTATACGGGAAAATTTGGTGGTGAATGGACAGCGCGTGTAAGT
GTGACACCAAAAAATCCTGCTGCTATCACTGAACCAATCTCACTGATTTGGTATGCTGCA
CTTGATGAGAAAAGTGAAGGAAATTTGAAAGCAACATATACAAATTCAATCTATGGGATA
GAAGGTGATACTCGTGGATTGGGAAGTTTCAAAGTCAATTTACACAACTCTAAAGGCAAC
ATTATAAAACAATCATACTTGAGTACAGTTGCTCCAAGCCTACAATATCTTAAAGAAACT
GTTCTTTCAAATCTACGACTTGCAAGCGATAAGATGACTAAAGAAAAATTTATAATTTTA
GCAGGCGATATGTTAGATGATAATACTAAACCGAATTTCGTTGCGCTCCAATTAAACGTT
GAAATTCCCTTCACTCTAGACATAACATTCCAAGATGTATCAAATATGAGTTCATTTTCC
GACGACTTTGTGGCATTGCCTGTCGGCGATGACTATTCAAAATTATTAGCAAAAAAGCGT
AAAGAGTTTGAAACAAAATTTTCAGACATTTTTCAATTACAACAAAAGGGATATTCGAAA
TTTGAAATTAAAGCAGCAGAGGCAGCACTTTCAAATATGTTGGGAAGTATAGGATATTTT
TATGGTGCATCAAAAGTTCAAAGTAATTATAATAAGGGACCAGTTCCATATTGGAAAGCA
CCTCTTTTAACAGCCGTACCATCAAGGTCATTTTTTCCTCGAGGATTTTTATGGGATGAA
GGATTTCATGGTCTACTGATTTCTACTTGGGATTTGGATATTGAGTTAGATATTATCAGT
CATTGGTTTGATCTCATTAATATCGAAGGTTGGATTCCTCGTGAACAAATTCTTGGTGTT
GAAGCTGTTGCTCGTGTACCAGAACAGTTTGTTATTCAACATAATACAAATGCAAATCCA
CCAACCTTCTTTTTAGTACTGAAACATATGCTTGACAATTATCCTGAAGAGATGTTGAAA
ACAAATAGATTGCAAATACTTGAACGTGTTTACCCAAGATTACATACATGGTTCCAATGG
TTCAATACGACACAGAAAGGCGAAGTTCTTGGAACATATCGATGGAAAGGTCGTCAAGCT
GATAGCATTCATGAATTAAATCCGAAAACACTCACAAGTGGTCTAGACGATTTTCCAAGG
TCATCACATCCAACTGATAATGAGCGTCATGTTGATTTGCGTTGTTGGATCACGCTAGCA
GCAGGTGTAATGAAACAATTGGGATCTATGTTGGGTAAAAATGTTGAAAAATATGAAGAA
ACTTACAATTATCTCTCAGATAATTTGCTTCTGCAAGAGCAACATTATTCTACGAAAGCA
AAACAATTTGCCGATTATGGATTGCATACTGATTCGACATCTCTTAAACGACCTCCACCG
CCACCATTAAATCCAAATCGAAGTCCATACGATCCTCCACCACCTGCTCCAGATATGATT
CGTGTTGTTTACGGACATCCTGAATTGAGATATGTAGATACAACATTTGGTTACGTAAAT
CTCTTTCCATTTTTGCTTCAGATAATTGAACCTTATAATCCCATCCTCGGAGTTATTCTT
ACTAAATTAAAAGATCCTGAATTATTATGGACAAAGTATGGATTGCGTTCTTTAGCTAAA
ACGTCACCACTTTATATGAAACGCAACACAGAACATGATCCACCATATTGGCGCGGTCAG
ATATGGATAAATATCAATTACCTTGCTCTAAAGAGCTTGTACTATTATAAGAGTCAGTCA
GGGCCATTTGCCGAACAAGCCAAAGATGTTTACACAGAATTACGAAAAAATGTAGTTTCA
AATGTTATAAATCAATACAATTCGACTGGTTTCATTTGGGAACAATATAGTGATGGAGGT
GGCAAAGGATCAGGTTGTTATCCGTTCACTGGATGGTCAGCACTCTTTGTGATGATTATG
TCCGAAAAATATTAA
>g4935.t1 Gene=g4935 Length=844
MVRNRKQHQQNENSSKQKSTSSKNEEKASSSNSNSTSSTTTTHNSNSSPTFSSSRKMIPS
WYISIGVASIAVVMYFVYQGYLETRVNTPLDEKRIVPKQPDSEKFWNTYRANTYFGLKTR
DPNSMVLGLMWYFPNKLRPNGDGIRHWCKLEDNLKKYGWLQHDGKNFGIQEIHEDNYVLE
TSFIKFYTGKFGGEWTARVSVTPKNPAAITEPISLIWYAALDEKSEGNLKATYTNSIYGI
EGDTRGLGSFKVNLHNSKGNIIKQSYLSTVAPSLQYLKETVLSNLRLASDKMTKEKFIIL
AGDMLDDNTKPNFVALQLNVEIPFTLDITFQDVSNMSSFSDDFVALPVGDDYSKLLAKKR
KEFETKFSDIFQLQQKGYSKFEIKAAEAALSNMLGSIGYFYGASKVQSNYNKGPVPYWKA
PLLTAVPSRSFFPRGFLWDEGFHGLLISTWDLDIELDIISHWFDLINIEGWIPREQILGV
EAVARVPEQFVIQHNTNANPPTFFLVLKHMLDNYPEEMLKTNRLQILERVYPRLHTWFQW
FNTTQKGEVLGTYRWKGRQADSIHELNPKTLTSGLDDFPRSSHPTDNERHVDLRCWITLA
AGVMKQLGSMLGKNVEKYEETYNYLSDNLLLQEQHYSTKAKQFADYGLHTDSTSLKRPPP
PPLNPNRSPYDPPPPAPDMIRVVYGHPELRYVDTTFGYVNLFPFLLQIIEPYNPILGVIL
TKLKDPELLWTKYGLRSLAKTSPLYMKRNTEHDPPYWRGQIWININYLALKSLYYYKSQS
GPFAEQAKDVYTELRKNVVSNVINQYNSTGFIWEQYSDGGGKGSGCYPFTGWSALFVMIM
SEKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g4935.t1 | Gene3D | G3DSA:2.70.98.110 | - | 96 | 375 | 6.3E-49 |
| 8 | g4935.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 50 | - |
| 7 | g4935.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 13 | 50 | - |
| 3 | g4935.t1 | PANTHER | PTHR10412:SF11 | MANNOSYL-OLIGOSACCHARIDE GLUCOSIDASE | 41 | 844 | 0.0 |
| 4 | g4935.t1 | PANTHER | PTHR10412 | MANNOSYL-OLIGOSACCHARIDE GLUCOSIDASE | 41 | 844 | 0.0 |
| 1 | g4935.t1 | Pfam | PF16923 | Glycosyl hydrolase family 63 N-terminal domain | 105 | 300 | 2.8E-46 |
| 2 | g4935.t1 | Pfam | PF03200 | Glycosyl hydrolase family 63 C-terminal domain | 350 | 842 | 2.3E-201 |
| 10 | g4935.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 60 | - |
| 12 | g4935.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 61 | 78 | - |
| 11 | g4935.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 79 | 844 | - |
| 6 | g4935.t1 | SUPERFAMILY | SSF48208 | Six-hairpin glycosidases | 343 | 844 | 1.53E-65 |
| 5 | g4935.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 60 | 82 | - |
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:0004573 | mannosyl-oligosaccharide glucosidase activity | MF |
| GO:0009311 | oligosaccharide metabolic process | BP |
| GO:0005975 | carbohydrate metabolic process | BP |
KEGG
Orthology
- This transcript has been annotated with K01228 (mannosyl-oligosaccharide glucosidase)
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.
