Gene loci information

Transcript annotation

  • This transcript has been annotated as GTP-binding protein SAR1b.

Parent gene

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.t61 TSS g1978.t61 14174170 14174170
chr_3 g1978 g1978.t61 isoform g1978.t61 14174427 14176064
chr_3 g1978 g1978.t61 exon g1978.t61.exon1 14174427 14174560
chr_3 g1978 g1978.t61 cds g1978.t61.CDS1 14174467 14174560
chr_3 g1978 g1978.t61 exon g1978.t61.exon2 14174772 14174834
chr_3 g1978 g1978.t61 cds g1978.t61.CDS2 14174772 14174834
chr_3 g1978 g1978.t61 exon g1978.t61.exon3 14175073 14175494
chr_3 g1978 g1978.t61 cds g1978.t61.CDS3 14175073 14175494
chr_3 g1978 g1978.t61 exon g1978.t61.exon4 14175559 14176064
chr_3 g1978 g1978.t61 cds g1978.t61.CDS4 14175559 14175675
chr_3 g1978 g1978.t61 TTS g1978.t61 14176066 14176066

Sequences

>g1978.t61 Gene=g1978 Length=1125
ACTATACTGCTTTATATTTTAAAAGTGTGATTGCTTACGAATGAAGAAAATTACTGACGA
TGATCAAAATATTAATTTTGATTGTATGCAATATCTCGAAACACAAAAACTCATCATTTC
TTCTTGTGTAAACTATTACAGCAAATTATTCACAATGTTCATTTGGGACTGGTTCACTGG
TGTTTTAGGATATTTGGGATTATGGAAGAAGTCGGGCAAATTATTATTTCTCGGATTAGA
TAATGCTGGTAAAACAACTTTATTACATATGCTTAAGGACGACAGATTAGCACAACATGT
TCCAACACTTCATCCAACGTCAGAAGAATTGTCTATAGGCAATATGCGCTTCACAACTTT
CGATTTAGGTGGTCACACACAGGCACGTCGTGTGTGGAAGGACTATTTTCCAGCTGTTGA
TGCAATTGTCTTCTTAATTGATGCATGGGATCGTAGTCGTTTTCAAGAGAGCAAAAATGA
ATTGGATTCATTGTTAACTGATGAAGCATTATCGAATTGTCCCGTTCTCATATTGGGAAA
TAAAATTGACAAACCGGGAGCTGCCAGTGAAGACGAATTGAGAAATTTTTATGGACTTTA
TCAACTTACAACAGGAAAGGGAAAAATTTCAAGATCAGATTTAGCAGGCCGTCCATTAGA
ACTTTTTATGTGCTCGGTGCTGAAGAGACAAGGATATGGTGAAGGTTTTCGCTGGTTAGC
TCAATATATCGATTAAAAATTATGAAGTCGACCATAATATTTTTAAATCAACCAACAACA
ACAATAATTAAAAAGCGTAAAGTTTCAAAATTCCCAACGCAAAGGTTTCACAAAATGAAA
CAAATTTTTACAAATTAATTAATTTAATATGCAACATTTGTGAATGATATGATATCAAAT
TCTTCAAAAAAAGACATCGTGGGATACAATAAAATAAAAAAAATAGTGAAAGAATCCTTT
TTTAAACCATAATACCTAATTGTATAATGATTATCAACATATTTATATTTTTGGTTTCTG
AGCAACTTGATGTGTTATCATTACTTTTTTAAACTATTGGAATGAAATCTGCTTCAAAAA
AGGCCGTTTGAAATAATAAAAGGAAACAATCTTTTTCTCATAAAT

>g1978.t61 Gene=g1978 Length=231
MKKITDDDQNINFDCMQYLETQKLIISSCVNYYSKLFTMFIWDWFTGVLGYLGLWKKSGK
LLFLGLDNAGKTTLLHMLKDDRLAQHVPTLHPTSEELSIGNMRFTTFDLGGHTQARRVWK
DYFPAVDAIVFLIDAWDRSRFQESKNELDSLLTDEALSNCPVLILGNKIDKPGAASEDEL
RNFYGLYQLTTGKGKISRSDLAGRPLELFMCSVLKRQGYGEGFRWLAQYID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1978.t61 CDD cd00879 Sar1 40 230 1.9374E-135
9 g1978.t61 Gene3D G3DSA:3.40.50.300 - 59 230 8.8E-60
2 g1978.t61 PANTHER PTHR45684 RE74312P 39 230 2.0E-98
3 g1978.t61 PRINTS PR00328 GTP-binding SAR1 protein signature 60 83 3.2E-68
4 g1978.t61 PRINTS PR00328 GTP-binding SAR1 protein signature 88 112 3.2E-68
7 g1978.t61 PRINTS PR00328 GTP-binding SAR1 protein signature 115 140 3.2E-68
6 g1978.t61 PRINTS PR00328 GTP-binding SAR1 protein signature 160 181 3.2E-68
5 g1978.t61 PRINTS PR00328 GTP-binding SAR1 protein signature 204 228 3.2E-68
1 g1978.t61 Pfam PF00025 ADP-ribosylation factor family 46 230 1.1E-63
11 g1978.t61 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 35 -
12 g1978.t61 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 36 54 -
10 g1978.t61 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 55 231 -
18 g1978.t61 ProSiteProfiles PS51422 small GTPase SAR1 family profile. 52 230 31.336
15 g1978.t61 SMART SM00177 arf_sub_2 41 218 1.5E-17
16 g1978.t61 SMART SM00178 sar_sub_1 42 230 3.5E-112
8 g1978.t61 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 55 230 7.11E-46
17 g1978.t61 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 57 180 6.8E-16
14 g1978.t61 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 33 55 -

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

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.

Raw TPM values