Gene loci information

Transcript annotation

  • This transcript has been annotated as Ribosome maturation protein SBDS.

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 g2120 g2120.t4 TTS g2120.t4 15332117 15332117
chr_3 g2120 g2120.t4 isoform g2120.t4 15332161 15333042
chr_3 g2120 g2120.t4 exon g2120.t4.exon1 15332161 15332319
chr_3 g2120 g2120.t4 cds g2120.t4.CDS1 15332161 15332319
chr_3 g2120 g2120.t4 exon g2120.t4.exon2 15332390 15332855
chr_3 g2120 g2120.t4 cds g2120.t4.CDS2 15332390 15332855
chr_3 g2120 g2120.t4 exon g2120.t4.exon3 15332927 15333042
chr_3 g2120 g2120.t4 cds g2120.t4.CDS3 15332927 15333042
chr_3 g2120 g2120.t4 TSS g2120.t4 15333078 15333078

Sequences

>g2120.t4 Gene=g2120 Length=741
ATGTCAAAAATTTTTACTCCAACTAATCAAATTCGTTTGACAAATGTAGCTGTTGTTAGA
ATAAAGAAGCATGGAATGCGTTTTGAGATAGCATGTTACAAAAATAAAGTTCAATCCGAA
AAAGATTTGTCAGAAGTTTTACAAACTGAAACGGTGTTTGCGAATGTATCAAAAGGACAA
GTTGCAAAAAAGGAAGATCTTATAAAAGCATTTGGAAAAGATGATCAAGTAGAAATTTGC
AAAGAAATTTTAGCAAAAGGCGAACTTCAAGTAAGCGAGAAAGAAAGGCATGCAAATTTA
GAGTCGACATTTAAAGAAATTGCTACAATGGTCTCTGATAAGTGTGTTAATCCTGAAACA
AATCGCGCATATCCAGTGACAATTATTGAGAAAGCCATGAAAGATGCTCATTATTCCATC
AAACCGAATAAGAACGTAAAAAGTCAGGCCTTGGACGTTATAAAACTTTTGAAGCAAAGC
ATCCCGATAGAAAAAGCTCAGATGCGAGTGAAAATTACAGTTACAAACTGCAAAGATAAA
AAGCTTCGTTTTGATGATATTCCTAAATTATTAAAAGTTAAGGAAAGTGAAAGCTGGACA
GCAGGAAATGGTAATATCGTTGCGTTGATTGATCCAGGAAATTATAAAATTATAGAAAGT
CTTCACTCAACAAGCAGAGGGGAGGTTACCATCGAAGTTCTTGATTTAAAACACATTAAA
GAAGATGAAGAAGTATTGTAA

>g2120.t4 Gene=g2120 Length=246
MSKIFTPTNQIRLTNVAVVRIKKHGMRFEIACYKNKVQSEKDLSEVLQTETVFANVSKGQ
VAKKEDLIKAFGKDDQVEICKEILAKGELQVSEKERHANLESTFKEIATMVSDKCVNPET
NRAYPVTIIEKAMKDAHYSIKPNKNVKSQALDVIKLLKQSIPIEKAQMRVKITVTNCKDK
KLRFDDIPKLLKVKESESWTAGNGNIVALIDPGNYKIIESLHSTSRGEVTIEVLDLKHIK
EDEEVL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2120.t4 Gene3D G3DSA:3.30.1250.10 - 1 90 0
9 g2120.t4 Gene3D G3DSA:1.10.10.900 - 94 166 0
8 g2120.t4 Gene3D G3DSA:3.30.70.240 - 167 246 0
3 g2120.t4 PANTHER PTHR10927 RIBOSOME MATURATION PROTEIN SBDS 1 245 0
4 g2120.t4 PANTHER PTHR10927:SF1 RIBOSOME MATURATION PROTEIN SBDS 1 245 0
2 g2120.t4 Pfam PF01172 Shwachman-Bodian-Diamond syndrome (SBDS) protein 15 97 0
1 g2120.t4 Pfam PF09377 SBDS protein C-terminal domain 104 220 0
5 g2120.t4 SUPERFAMILY SSF89895 FYSH domain 11 90 0
6 g2120.t4 SUPERFAMILY SSF109728 Hypothetical protein AF0491, middle domain 91 164 0
10 g2120.t4 TIGRFAM TIGR00291 RNA_SBDS: rRNA metabolism protein, SBDS family 10 233 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

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