General information for g2120.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribosome maturation protein SBDS.
Parent gene
- The parent gene g2120 is located on chr_3: 15333042..15334291 (- 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 | g2120 | g2120.t1 | TTS | g2120.t1 | 15332117 | 15332117 |
| chr_3 | g2120 | g2120.t1 | isoform | g2120.t1 | 15332161 | 15333042 |
| chr_3 | g2120 | g2120.t1 | exon | g2120.t1.exon1 | 15332161 | 15332319 |
| chr_3 | g2120 | g2120.t1 | cds | g2120.t1.CDS1 | 15332161 | 15332319 |
| chr_3 | g2120 | g2120.t1 | exon | g2120.t1.exon2 | 15332390 | 15332855 |
| chr_3 | g2120 | g2120.t1 | cds | g2120.t1.CDS2 | 15332390 | 15332855 |
| chr_3 | g2120 | g2120.t1 | exon | g2120.t1.exon3 | 15332912 | 15333042 |
| chr_3 | g2120 | g2120.t1 | cds | g2120.t1.CDS3 | 15332912 | 15333042 |
| chr_3 | g2120 | g2120.t1 | TSS | g2120.t1 | 15333078 | 15333078 |
Sequences
>g2120.t1 Gene=g2120 Length=756
ATGTCAAAAATTTTTACTCCAACTAATCAAATTCGTTTGACAAATGTAGCTGTTGTTAGA
ATAAAGAAGCATGGAATGCGTTTTGAGATAGCATGTTACAAAAATAAAGTTCAATCGTGG
AGAGCTCAAACCGAAAAAGATTTGTCAGAAGTTTTACAAACTGAAACGGTGTTTGCGAAT
GTATCAAAAGGACAAGTTGCAAAAAAGGAAGATCTTATAAAAGCATTTGGAAAAGATGAT
CAAGTAGAAATTTGCAAAGAAATTTTAGCAAAAGGCGAACTTCAAGTAAGCGAGAAAGAA
AGGCATGCAAATTTAGAGTCGACATTTAAAGAAATTGCTACAATGGTCTCTGATAAGTGT
GTTAATCCTGAAACAAATCGCGCATATCCAGTGACAATTATTGAGAAAGCCATGAAAGAT
GCTCATTATTCCATCAAACCGAATAAGAACGTAAAAAGTCAGGCCTTGGACGTTATAAAA
CTTTTGAAGCAAAGCATCCCGATAGAAAAAGCTCAGATGCGAGTGAAAATTACAGTTACA
AACTGCAAAGATAAAAAGCTTCGTTTTGATGATATTCCTAAATTATTAAAAGTTAAGGAA
AGTGAAAGCTGGACAGCAGGAAATGGTAATATCGTTGCGTTGATTGATCCAGGAAATTAT
AAAATTATAGAAAGTCTTCACTCAACAAGCAGAGGGGAGGTTACCATCGAAGTTCTTGAT
TTAAAACACATTAAAGAAGATGAAGAAGTATTGTAA
>g2120.t1 Gene=g2120 Length=251
MSKIFTPTNQIRLTNVAVVRIKKHGMRFEIACYKNKVQSWRAQTEKDLSEVLQTETVFAN
VSKGQVAKKEDLIKAFGKDDQVEICKEILAKGELQVSEKERHANLESTFKEIATMVSDKC
VNPETNRAYPVTIIEKAMKDAHYSIKPNKNVKSQALDVIKLLKQSIPIEKAQMRVKITVT
NCKDKKLRFDDIPKLLKVKESESWTAGNGNIVALIDPGNYKIIESLHSTSRGEVTIEVLD
LKHIKEDEEVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g2120.t1 | Gene3D | G3DSA:3.30.1250.10 | - | 1 | 95 | 0 |
| 9 | g2120.t1 | Gene3D | G3DSA:1.10.10.900 | - | 99 | 171 | 0 |
| 8 | g2120.t1 | Gene3D | G3DSA:3.30.70.240 | - | 172 | 251 | 0 |
| 3 | g2120.t1 | PANTHER | PTHR10927 | RIBOSOME MATURATION PROTEIN SBDS | 1 | 250 | 0 |
| 4 | g2120.t1 | PANTHER | PTHR10927:SF1 | RIBOSOME MATURATION PROTEIN SBDS | 1 | 250 | 0 |
| 2 | g2120.t1 | Pfam | PF01172 | Shwachman-Bodian-Diamond syndrome (SBDS) protein | 15 | 102 | 0 |
| 1 | g2120.t1 | Pfam | PF09377 | SBDS protein C-terminal domain | 109 | 225 | 0 |
| 5 | g2120.t1 | SUPERFAMILY | SSF89895 | FYSH domain | 11 | 95 | 0 |
| 6 | g2120.t1 | SUPERFAMILY | SSF109728 | Hypothetical protein AF0491, middle domain | 96 | 169 | 0 |
| 10 | g2120.t1 | TIGRFAM | TIGR00291 | RNA_SBDS: rRNA metabolism protein, SBDS family | 10 | 238 | 0 |
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:0042254 | ribosome biogenesis | BP |
| GO:0042256 | mature ribosome assembly | BP |
KEGG
Orthology
- This transcript has been annotated with K14574 (ribosome maturation protein SDO1)
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.
