General information for g10553.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nucleoporin Nup35.
Parent gene
- The parent gene g10553 is located on chr_1: 10450720..10451874 (- 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 | g10553 | g10553.t3 | isoform | g10553.t3 | 10450720 | 10451709 |
| chr_1 | g10553 | g10553.t3 | exon | g10553.t3.exon1 | 10450720 | 10451709 |
| chr_1 | g10553 | g10553.t3 | TTS | g10553.t3 | 10450741 | 10450741 |
| chr_1 | g10553 | g10553.t3 | cds | g10553.t3.CDS1 | 10450835 | 10451689 |
| chr_1 | g10553 | g10553.t3 | TSS | g10553.t3 | 10451964 | 10451964 |
Sequences
>g10553.t3 Gene=g10553 Length=990
CAACTGCATCACCTTCTAGCATGCAACAAAAGTTTTTGACAAGTTTACAAAGTCCCAATC
CTATTTTTAATTCATCAATGAACCAATCATTTAACAATATTCATCATCATCAACAACAAA
TTTTTCAAACACAAAATCCAGCAAACAATTCAGCAGCAAATAACAATAATAATAGTATTT
CTGGACCACCCATCAATTCACTCTTTGATAATTTAAGAAACGAAATGAATTTTCAAACTC
CCACAAAAAGCTTCTATCATCAATCAATAATTCATCAGGATACTCCGCAACCTATGCATA
ATAATTCTGAATTTAATCAATCACGTATATTATCACCTATTCCACTTTCTTTCCCATCTG
GGGCTGTTAATAATGATTTTAATACTTCCACTTCCTTTCAAAACCTTATGCAGCAATCTG
GTGCAATTTACAACAATATAAATCAATCAATGAATGGCTATAGTCAAAAGGATTTTTGGG
TAACAGTTTTTGGCTTTCCGTCTGAAGCTCTAACAATCGTTCTATCACATTTTTCTGGTT
GTGGAACAATTCTTGAGAAAGTCTGTTCATCGGGCAATTGGGTTCATTTAAGATATTCTT
CTCGTGCCGAATGCGATAAGTCTCTTCTTTATAATGGAAAAATTATTGGAAATAATTTAA
TGATTGGTGTTGTTCGATGTGAAGACGAATCAATTACAGAAAAAGAAAACATGAATTATA
ATCCTCAAACTTCCATCACTAAAATTCGTTCATTGACTCAAGCTGCATACAAGTCGGTGC
GTGATGAGACGGAAGTTGTACCAAGTGGTATCGAAGAGCCAAAAAAGACAACAGGCATAG
TTAATAAAGCGATGGATCTTATTTTTGGATGGTAAATGCAAATACTTTCATATTTTAAAC
AACCTTTCATTTGTTATGTCCAATTTATATTTCTTTTTCTTAAAATAAAATAACGATATT
AAAAACTTTAAAGTTCTTATTCTTCTTAGT
>g10553.t3 Gene=g10553 Length=284
MQQKFLTSLQSPNPIFNSSMNQSFNNIHHHQQQIFQTQNPANNSAANNNNNSISGPPINS
LFDNLRNEMNFQTPTKSFYHQSIIHQDTPQPMHNNSEFNQSRILSPIPLSFPSGAVNNDF
NTSTSFQNLMQQSGAIYNNINQSMNGYSQKDFWVTVFGFPSEALTIVLSHFSGCGTILEK
VCSSGNWVHLRYSSRAECDKSLLYNGKIIGNNLMIGVVRCEDESITEKENMNYNPQTSIT
KIRSLTQAAYKSVRDETEVVPSGIEEPKKTTGIVNKAMDLIFGW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10553.t3 | CDD | cd12441 | RRM_Nup53_like | 151 | 222 | 0.000 |
| 4 | g10553.t3 | Gene3D | G3DSA:3.30.70.330 | - | 148 | 220 | 0.000 |
| 2 | g10553.t3 | PANTHER | PTHR21527 | NUCLEOPORIN NUP35 | 6 | 284 | 0.000 |
| 6 | g10553.t3 | PIRSF | PIRSF038119 | NUP53 | 3 | 284 | 0.000 |
| 1 | g10553.t3 | Pfam | PF05172 | Nup53/35/40-type RNA recognition motif | 149 | 224 | 0.000 |
| 5 | g10553.t3 | ProSiteProfiles | PS51472 | RNA-recognition motif (RRM) Nup35-type domain profile. | 148 | 227 | 29.289 |
| 3 | g10553.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 150 | 225 | 0.000 |
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:0031965 | nuclear membrane | CC |
| GO:0006913 | nucleocytoplasmic transport | BP |
| GO:0017056 | structural constituent of nuclear pore | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
