General information for g3523.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nucleolar GTP-binding protein 2.
Parent gene
- The parent gene g3523 is located on chr_3: 26191919..26194159 (+ 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 | g3523 | g3523.t1 | isoform | g3523.t1 | 26189606 | 26191919 |
| chr_3 | g3523 | g3523.t1 | exon | g3523.t1.exon1 | 26189606 | 26189633 |
| chr_3 | g3523 | g3523.t1 | cds | g3523.t1.CDS1 | 26189606 | 26189633 |
| chr_3 | g3523 | g3523.t1 | exon | g3523.t1.exon2 | 26189695 | 26189712 |
| chr_3 | g3523 | g3523.t1 | cds | g3523.t1.CDS2 | 26189695 | 26189712 |
| chr_3 | g3523 | g3523.t1 | exon | g3523.t1.exon3 | 26189784 | 26190767 |
| chr_3 | g3523 | g3523.t1 | cds | g3523.t1.CDS3 | 26189784 | 26190767 |
| chr_3 | g3523 | g3523.t1 | exon | g3523.t1.exon4 | 26190823 | 26191016 |
| chr_3 | g3523 | g3523.t1 | cds | g3523.t1.CDS4 | 26190823 | 26191016 |
| chr_3 | g3523 | g3523.t1 | exon | g3523.t1.exon5 | 26191071 | 26191919 |
| chr_3 | g3523 | g3523.t1 | cds | g3523.t1.CDS5 | 26191071 | 26191919 |
| chr_3 | g3523 | g3523.t1 | TTS | g3523.t1 | 26192027 | 26192027 |
| chr_3 | g3523 | g3523.t1 | TSS | g3523.t1 | NA | NA |
Sequences
>g3523.t1 Gene=g3523 Length=2073
ATGAAATTTCTGACACGAATACATTCCCTTGTCAACAAAAACACATTTAAAACAATGGCA
AAGACAACTTCAAGATCAGGCCCTCCAAGAAAGGAAGGAAGAATGAATAAAAGCAGTCAT
TCATTGAATCCTGAGCGATCAGCAGAAAATGTTAAAGGCGGAAGGGTAAGAACAAAATCT
ACAATCCAGAGATTGCAAATGTACAGAAACTTTAAAGCAAAAAGAGATCGTAGAGGAAAA
ATAATTAAAGCAGCACCATTTCAAGGATGGTTAGCATCTGGCACACAATCAAGAGTCGAA
CCGTCACCAAAATGGTTCAGCAATTCAAGAGTTATTTCACAATCAGCATTACAGAAATTT
CAAGATGAAATGGGAAAAGTTATGAAAGATCCCTATCAAGTAGTGATGAAACCAACAAAT
TTACCAATTACTCTGCTTAATGAAAGTGCAAAATATCAGCGAGTTCATTTACTTGATACA
CAATCATTTTCTTCAACATTTGGTCCTAAAGCTCAACGCAAAAGACCAACTTTGAAAGTT
AAAGATTTAGATGATATGGTGAAAGCAGCAGAGCAAGCATCAGAAACATATAATGACGAG
AAAGATTATGATTTGATCAGAGACGATGGTGGAGTTCGTCAAATGCCACGAGACTGGGTG
TTTGCTGCTGGCCAGAGTAAAAGAATTTGGAATGAATTGCACAAAGTAATTGATTCAGCT
GATGTGCTTTTACAAGTTTTAGACGCTCGTGATCCAATGGGAACAAGATCAAAATATATA
GAGGAATTTTTGCGAAAAGAAAAGAAACATAAACATCTTTTCTTTGTTCTTAATAAAGTT
GATTTGGTGCCGATTTGGGTAACACAACGATGGGTGGCAATTCTTTCCTCAGAATATCCT
ACAATTGCTTTTCATGCATCTTTGACACATCCTTTTGGTAAAGGTGCACTTATTAATCTT
TTGCGTCAAGTTGGAAAACTTCATGTTGACAAAAAACAAATCAGCATAGGTTTCATAGGC
TATCCTAATGTTGGTAAATCTTCTGTCATTAATGCACTTCGTGGAAAGAAAGTTTGTAAT
GTAGCTCCAATTGCTGGTGAAACAAAAGTATGGCAATATATTACTTTAATGAAAAGAATA
TTCCTAATTGACTGTCCAGGAGTAGTTTATCCAACAGCAGAAACTGATGCAGAAAAAGTG
CTAAAAGGAGTTGTTCGTGTAGAATTGGTTACAAATCCTGAAGATTATGTTGAAGAAGTT
TTAAAACGTGTACGAAAAGAATATATGGGAAAGACTTATGGCATTACAGAATATGAAGAT
CACATCGATTTCCTAGAACAGCTTGCAAAAAAAACCGGAAAATTGCTTAAAGGTGGTGAA
CCTGATGTCACTGCCGCTGCAAAAATGATTCTTAATGACTGGCAAAGAGGTAAATTACCG
TTTTATGTTGCACCAGAAGGATTTGAAGTGCCAAAATCAAAAGAACCAGCAACTATTGAG
AAGACGACAGAAGAGAACAAAAATGTAACAATTCCTGAAGATGATGAAACAAAGAGTATT
GCAACTGCAGTTTCTGAATCCGTTTTAAAAGGTCGTGCACTTAAGCAGTTACAAGATTAT
CGCAAAATTCGTGTTAATCTCGAATTTGAAGCAGAAGATGAAAAAGAGTTGGATTTGGAT
GAAATTCGAGAATATGAAGAATACAAAAGACTTCAATCTGAAAAGAAGAAAAAACGTAAA
TTTGACAATGATGATGGAGAAGATTCATCAGACATCAGTGATTTTTACTCAGAGGATGAA
TATGATGAAGAAAAAGGACGTGTTGTTCATAGAAGTGCAGGCACTAAAATTAAAACAAAA
CCTGATACTAAGAAACAGAAAACAACAAGTGGATTTTTCGATGTAGAAGATGTCAATGTA
ACTACTAAGAAGATTACTACACCGAAAAAATTAACAGCTAAACAGAGAAGAGCTATTGAG
AGAAAAGAGAAGCCAAAAAAAGTTGGAAGCAATTTCTACGATGTTGTCAATGTAAAAAAC
AAAACGAAAAGCAAGAAATTTCAAGGAAAATAG
>g3523.t1 Gene=g3523 Length=690
MKFLTRIHSLVNKNTFKTMAKTTSRSGPPRKEGRMNKSSHSLNPERSAENVKGGRVRTKS
TIQRLQMYRNFKAKRDRRGKIIKAAPFQGWLASGTQSRVEPSPKWFSNSRVISQSALQKF
QDEMGKVMKDPYQVVMKPTNLPITLLNESAKYQRVHLLDTQSFSSTFGPKAQRKRPTLKV
KDLDDMVKAAEQASETYNDEKDYDLIRDDGGVRQMPRDWVFAAGQSKRIWNELHKVIDSA
DVLLQVLDARDPMGTRSKYIEEFLRKEKKHKHLFFVLNKVDLVPIWVTQRWVAILSSEYP
TIAFHASLTHPFGKGALINLLRQVGKLHVDKKQISIGFIGYPNVGKSSVINALRGKKVCN
VAPIAGETKVWQYITLMKRIFLIDCPGVVYPTAETDAEKVLKGVVRVELVTNPEDYVEEV
LKRVRKEYMGKTYGITEYEDHIDFLEQLAKKTGKLLKGGEPDVTAAAKMILNDWQRGKLP
FYVAPEGFEVPKSKEPATIEKTTEENKNVTIPEDDETKSIATAVSESVLKGRALKQLQDY
RKIRVNLEFEAEDEKELDLDEIREYEEYKRLQSEKKKKRKFDNDDGEDSSDISDFYSEDE
YDEEKGRVVHRSAGTKIKTKPDTKKQKTTSGFFDVEDVNVTTKKITTPKKLTAKQRRAIE
RKEKPKKVGSNFYDVVNVKNKTKSKKFQGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3523.t1 | CDD | cd01858 | NGP_1 | 232 | 388 | 8.01741E-118 |
| 10 | g3523.t1 | Coils | Coil | Coil | 180 | 200 | - |
| 8 | g3523.t1 | Gene3D | G3DSA:3.40.50.300 | - | 220 | 390 | 1.8E-43 |
| 9 | g3523.t1 | Gene3D | G3DSA:1.10.1580.10 | - | 393 | 483 | 2.2E-15 |
| 13 | g3523.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 19 | 57 | - |
| 12 | g3523.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 573 | 607 | - |
| 3 | g3523.t1 | PANTHER | PTHR11089 | GTP-BINDING PROTEIN-RELATED | 28 | 688 | 4.7E-255 |
| 4 | g3523.t1 | PANTHER | PTHR11089:SF9 | NUCLEOLAR GTP-BINDING PROTEIN 2 | 28 | 688 | 4.7E-255 |
| 5 | g3523.t1 | PRINTS | PR00326 | GTP1/OBG GTP-binding protein family signature | 336 | 356 | 1.4E-6 |
| 6 | g3523.t1 | PRINTS | PR00326 | GTP1/OBG GTP-binding protein family signature | 382 | 397 | 1.4E-6 |
| 2 | g3523.t1 | Pfam | PF08153 | NGP1NT (NUC091) domain | 67 | 197 | 1.3E-48 |
| 1 | g3523.t1 | Pfam | PF01926 | 50S ribosome-binding GTPase | 336 | 410 | 1.5E-13 |
| 14 | g3523.t1 | ProSiteProfiles | PS51721 | Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. | 230 | 391 | 32.157 |
| 7 | g3523.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 226 | 466 | 9.32E-42 |
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:0005730 | nucleolus | CC |
| GO:0005525 | GTP binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14537 (nuclear GTP-binding protein)
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.
