General information for g1978.t49
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GTP-binding protein SAR1.
Parent gene
- The parent gene g1978 is located on chr_3: 14175617..14176064 (+ 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 | g1978 | g1978.t49 | isoform | g1978.t49 | 14174162 | 14176064 |
| chr_3 | g1978 | g1978.t49 | exon | g1978.t49.exon1 | 14174162 | 14174283 |
| chr_3 | g1978 | g1978.t49 | TSS | g1978.t49 | 14174170 | 14174170 |
| chr_3 | g1978 | g1978.t49 | exon | g1978.t49.exon2 | 14174772 | 14174834 |
| chr_3 | g1978 | g1978.t49 | cds | g1978.t49.CDS1 | 14174792 | 14174834 |
| chr_3 | g1978 | g1978.t49 | exon | g1978.t49.exon3 | 14175073 | 14175494 |
| chr_3 | g1978 | g1978.t49 | cds | g1978.t49.CDS2 | 14175073 | 14175494 |
| chr_3 | g1978 | g1978.t49 | exon | g1978.t49.exon4 | 14175573 | 14176064 |
| chr_3 | g1978 | g1978.t49 | cds | g1978.t49.CDS3 | 14175573 | 14175641 |
| chr_3 | g1978 | g1978.t49 | TTS | g1978.t49 | 14176066 | 14176066 |
Sequences
>g1978.t49 Gene=g1978 Length=1099
TCTCACCAAAGTGAATAAAAATTGTCAAAAAGTTCCAGGTTGGAATTTTTTCATTATTTT
AAAATACTGCGTTAATTGATAAGTTAGCTAAGAAAATTATAGTAATTTAGTTGGTTTAAG
AGATTACAGCAAATTATTCACAATGTTCATTTGGGACTGGTTCACTGGTGTTTTAGGATA
TTTGGGATTATGGAAGAAGTCGGGCAAATTATTATTTCTCGGATTAGATAATGCTGGTAA
AACAACTTTATTACATATGCTTAAGGACGACAGATTAGCACAACATGTTCCAACACTTCA
TCCAACGTCAGAAGAATTGTCTATAGGCAATATGCGCTTCACAACTTTCGATTTAGGTGG
TCACACACAGGCACGTCGTGTGTGGAAGGACTATTTTCCAGCTGTTGATGCAATTGTCTT
CTTAATTGATGCATGGGATCGTAGTCGTTTTCAAGAGAGCAAAAATGAATTGGATTCATT
GTTAACTGATGAAGCATTATCGAATTGTCCCGTTCTCATATTGGGAAATAAAATTGACAA
ACCGGGAGCTGCCAGTGAAGACGAATTGAGAAATTTTTATGGACTTTATCAACTTACAAC
AGGAAAGATCAGATTTAGCAGGCCGTCCATTAGAACTTTTTATGTGCTCGGTGCTGAAGA
GACAAGGATATGGTGAAGGTTTTCGCTGGTTAGCTCAATATATCGATTAAAAATTATGAA
GTCGACCATAATATTTTTAAATCAACCAACAACAACAATAATTAAAAAGCGTAAAGTTTC
AAAATTCCCAACGCAAAGGTTTCACAAAATGAAACAAATTTTTACAAATTAATTAATTTA
ATATGCAACATTTGTGAATGATATGATATCAAATTCTTCAAAAAAAGACATCGTGGGATA
CAATAAAATAAAAAAAATAGTGAAAGAATCCTTTTTTAAACCATAATACCTAATTGTATA
ATGATTATCAACATATTTATATTTTTGGTTTCTGAGCAACTTGATGTGTTATCATTACTT
TTTTAAACTATTGGAATGAAATCTGCTTCAAAAAAGGCCGTTTGAAATAATAAAAGGAAA
CAATCTTTTTCTCATAAAT
>g1978.t49 Gene=g1978 Length=177
MFIWDWFTGVLGYLGLWKKSGKLLFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELS
IGNMRFTTFDLGGHTQARRVWKDYFPAVDAIVFLIDAWDRSRFQESKNELDSLLTDEALS
NCPVLILGNKIDKPGAASEDELRNFYGLYQLTTGKIRFSRPSIRTFYVLGAEETRIW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1978.t49 | CDD | cd00879 | Sar1 | 2 | 168 | 0.000 |
| 8 | g1978.t49 | Gene3D | G3DSA:3.40.50.300 | - | 21 | 174 | 0.000 |
| 2 | g1978.t49 | PANTHER | PTHR45684 | RE74312P | 1 | 157 | 0.000 |
| 6 | g1978.t49 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 22 | 45 | 0.000 |
| 5 | g1978.t49 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 50 | 74 | 0.000 |
| 4 | g1978.t49 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 77 | 102 | 0.000 |
| 3 | g1978.t49 | PRINTS | PR00328 | GTP-binding SAR1 protein signature | 122 | 143 | 0.000 |
| 1 | g1978.t49 | Pfam | PF00025 | ADP-ribosylation factor family | 8 | 154 | 0.000 |
| 13 | g1978.t49 | ProSiteProfiles | PS51422 | small GTPase SAR1 family profile. | 14 | 177 | 24.663 |
| 10 | g1978.t49 | SMART | SM00177 | arf_sub_2 | 3 | 177 | 0.000 |
| 11 | g1978.t49 | SMART | SM00178 | sar_sub_1 | 4 | 177 | 0.000 |
| 7 | g1978.t49 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 17 | 157 | 0.000 |
| 12 | g1978.t49 | TIGRFAM | TIGR00231 | small_GTP: small GTP-binding protein domain | 19 | 143 | 0.000 |
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:0006886 | intracellular protein transport | BP |
| GO:0005525 | GTP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K07953 (GTP-binding protein SAR1 [EC:3.6.5.-])
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