General information for g13880.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Large subunit GTPase 1-like protein.
Parent gene
- The parent gene g13880 is located on chr_1: 33090709..33092679 (- 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 | g13880 | g13880.t1 | TTS | g13880.t1 | 33090605 | 33090605 |
| chr_1 | g13880 | g13880.t1 | isoform | g13880.t1 | 33090709 | 33092679 |
| chr_1 | g13880 | g13880.t1 | exon | g13880.t1.exon1 | 33090709 | 33092529 |
| chr_1 | g13880 | g13880.t1 | cds | g13880.t1.CDS1 | 33090709 | 33092529 |
| chr_1 | g13880 | g13880.t1 | exon | g13880.t1.exon2 | 33092587 | 33092679 |
| chr_1 | g13880 | g13880.t1 | cds | g13880.t1.CDS2 | 33092587 | 33092679 |
| chr_1 | g13880 | g13880.t1 | TSS | g13880.t1 | 33092753 | 33092753 |
Sequences
>g13880.t1 Gene=g13880 Length=1914
ATGGTTGGTAAGAAAAAAGCTAATCAGCTTGGCCGATCACTTATGAAAGATCGATTTAGT
AACACAAATAAACGAAAAGTTGAAGAGAATATGCTTCATGTTGCTGATTTAAAAGATGGT
TACGATTGGGCAAAATTAAATCTTAATTCAGTTACTGAAGAAGATTCATTTCAAGAGTTT
TTAAGAAAAGCAGAATTGGCAGGAACCGAATTTACTGCTGAAAAGTTAAATATAAAATTT
GTTAATCCCAAATCATCGGCTGGTCTTCTATCAGATGCAGAATTTAAGAATGTTGAAAAG
CTTATTAATCAGCACAAGGATTCAATTAAAATTCCTCGTCGTCCAAAATGGACTAAAGAA
ACGACACCAGAAGAATTAAATCGAAATGAAAATCAAGCATTTTTAGAATGGAGAAGAGAT
TTAGCATTGTTAGCAGAGACTGAAGGTATTGTCATCACGCCATATGAAAAGAATTTAGAA
TTTTGGAGACAATTATGGCGTGTTATTGAGAGATCTGACGTTATCGTGCAGATTGTTGAT
GCTAGAAATCCTTTGCTTTTTAGAAATGAAGATTTGGAAAAGTATGTGAAAGAAGTGAAT
CCTGATAAACAAAACCTATTATTAATCAATAAAGCTGATTATTTAACGGATGAACAGAGA
GCAATCTGGGCAGAATATTTTGATAATCAAAATATAAAAGCTGTTTTCTTTTCTGCAATT
GAACAAGAGGAGAAAGATGCAAAATATAATAGTGACAGTTCAGATGATGAGGAGGAAGAT
GAAGAAGATGAAAGTGATTCGGAAACAGAAAATGAAGAAGAGACCGAAAAAATTTCAGTG
AATGACCTTAAAAATAAAATCGATGAAATTGCACAGAATATTGATGAAGCTGACAATTTG
TTGAATAAAATTATTGAAGATCCAACATCAGTTATGAAGTCTGAATCAATATCTGAAAAA
GTTCAAAAAGAAGTGTGTGCATCCAATAAGAATAATCCAAATATTCTTACTCGACTCGAG
TTAATTGAATTATTTAGAAGCATTCGTGCTACACATCCACTTTGTAAAGAGAAAGAAGCA
ATTGTGATTGGTCTAATTGGATTTCCTAATGTTGGTAAGAGTAGCACAATTAATGCACTT
TTACAAGCGAAGAAAGTCAGTGTGTCAGCGACACCTGGAAAAACGAAGCATTTTCAAACT
CTCTATCTTGAACGTGAAATAATTTTATGTGATTGCTGTGGTTTAGTGATGCCAACACTT
TGTTTCACAAAAGCTGACATGATTTTAAATGGAATTTTACCAATTGATCAAATGCGTGAT
TATGTACCTCCAATTAATACACTATGCACATTGATTCCTCGACACATATTAGAAGATACT
TATGGAATTTTAATTACAAAACCGTTGGAAGGTGAAGATCCAAGTAGACCACCACATTCT
GAAGAATTATTATTGGCATATGCATATAATAGAGGATTTATGACTGCCAATGGACAGCCT
GATCAGTCGAGAGCAGCTCGAAGAGTTTTAAAAGATTTTATTAATGGAAAGTTGCTCTAT
TGCAATTCACCACCAACTCACAATCAAAAAGAGTTTCACAAATATCCTGAGAGGGTTCAT
AAAGAAATTGAATTATCAAGTTTACCACCTAGACAACAACGTGCAATGAAACTTGTAACG
GGTGTCACGAGTAAAGATATTGATGATTTGTTTTTCGCATCAGAAAGTGCAAAATCACAT
GTTAAGGGAAGAAATTTGATGAATGAAAAGCAGCAGATAAGAATAAATCCAATTGGTGCT
CAAGCAATTGGTTCAACGTCTTCAATGATGACAATTGGAAAGAAAAGTAAAGCACCGAAA
AAAGAAAAACGAGAGAAATTAAGAAGAAAATATGCTCATTTAGATCAGCATTAA
>g13880.t1 Gene=g13880 Length=637
MVGKKKANQLGRSLMKDRFSNTNKRKVEENMLHVADLKDGYDWAKLNLNSVTEEDSFQEF
LRKAELAGTEFTAEKLNIKFVNPKSSAGLLSDAEFKNVEKLINQHKDSIKIPRRPKWTKE
TTPEELNRNENQAFLEWRRDLALLAETEGIVITPYEKNLEFWRQLWRVIERSDVIVQIVD
ARNPLLFRNEDLEKYVKEVNPDKQNLLLINKADYLTDEQRAIWAEYFDNQNIKAVFFSAI
EQEEKDAKYNSDSSDDEEEDEEDESDSETENEEETEKISVNDLKNKIDEIAQNIDEADNL
LNKIIEDPTSVMKSESISEKVQKEVCASNKNNPNILTRLELIELFRSIRATHPLCKEKEA
IVIGLIGFPNVGKSSTINALLQAKKVSVSATPGKTKHFQTLYLEREIILCDCCGLVMPTL
CFTKADMILNGILPIDQMRDYVPPINTLCTLIPRHILEDTYGILITKPLEGEDPSRPPHS
EELLLAYAYNRGFMTANGQPDQSRAARRVLKDFINGKLLYCNSPPTHNQKEFHKYPERVH
KEIELSSLPPRQQRAMKLVTGVTSKDIDDLFFASESAKSHVKGRNLMNEKQQIRINPIGA
QAIGSTSSMMTIGKKSKAPKKEKREKLRRKYAHLDQH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13880.t1 | CDD | cd01857 | HSR1_MMR1 | 161 | 418 | 2.36996E-69 |
| 6 | g13880.t1 | Coils | Coil | Coil | 280 | 307 | - |
| 5 | g13880.t1 | Gene3D | G3DSA:1.10.1580.10 | - | 425 | 518 | 1.8E-5 |
| 9 | g13880.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 281 | - |
| 8 | g13880.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 273 | - |
| 10 | g13880.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 605 | 637 | - |
| 2 | g13880.t1 | PANTHER | PTHR45709:SF2 | LARGE SUBUNIT GTPASE 1 HOMOLOG | 4 | 626 | 1.6E-200 |
| 3 | g13880.t1 | PANTHER | PTHR45709 | LARGE SUBUNIT GTPASE 1 HOMOLOG-RELATED | 4 | 626 | 1.6E-200 |
| 1 | g13880.t1 | Pfam | PF01926 | 50S ribosome-binding GTPase | 363 | 416 | 4.4E-12 |
| 11 | g13880.t1 | ProSiteProfiles | PS51721 | Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. | 162 | 418 | 36.228 |
| 4 | g13880.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 160 | 468 | 3.66E-37 |
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:0005525 | GTP binding | MF |
| GO:0003924 | GTPase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K14539 (large subunit GTPase 1 [EC:3.6.1.-])
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.
