General information for g10553.t2
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.t2 | isoform | g10553.t2 | 10450606 | 10451874 |
| chr_1 | g10553 | g10553.t2 | exon | g10553.t2.exon1 | 10450606 | 10451718 |
| chr_1 | g10553 | g10553.t2 | cds | g10553.t2.CDS1 | 10450835 | 10451718 |
| chr_1 | g10553 | g10553.t2 | exon | g10553.t2.exon2 | 10451778 | 10451874 |
| chr_1 | g10553 | g10553.t2 | cds | g10553.t2.CDS2 | 10451778 | 10451874 |
| chr_1 | g10553 | g10553.t2 | TSS | g10553.t2 | 10451964 | 10451964 |
| chr_1 | g10553 | g10553.t2 | TTS | g10553.t2 | NA | NA |
Sequences
>g10553.t2 Gene=g10553 Length=1210
ATGGAGAAAATGCAGCTTGGAAGCCCTCAAAATACCTATTTACCTAATTTTCTAATGGGA
GAACAAACGCCGACTAATCAACATCATCGTTCTTTTTCAAATTCACCAACTGCATCACCT
TCTAGCATGCAACAAAAGTTTTTGACAAGTTTACAAAGTCCCAATCCTATTTTTAATTCA
TCAATGAACCAATCATTTAACAATATTCATCATCATCAACAACAAATTTTTCAAACACAA
AATCCAGCAAACAATTCAGCAGCAAATAACAATAATAATAGTATTTCTGGACCACCCATC
AATTCACTCTTTGATAATTTAAGAAACGAAATGAATTTTCAAACTCCCACAAAAAGCTTC
TATCATCAATCAATAATTCATCAGGATACTCCGCAACCTATGCATAATAATTCTGAATTT
AATCAATCACGTATATTATCACCTATTCCACTTTCTTTCCCATCTGGGGCTGTTAATAAT
GATTTTAATACTTCCACTTCCTTTCAAAACCTTATGCAGCAATCTGGTGCAATTTACAAC
AATATAAATCAATCAATGAATGGCTATAGTCAAAAGGATTTTTGGGTAACAGTTTTTGGC
TTTCCGTCTGAAGCTCTAACAATCGTTCTATCACATTTTTCTGGTTGTGGAACAATTCTT
GAGAAAGTCTGTTCATCGGGCAATTGGGTTCATTTAAGATATTCTTCTCGTGCCGAATGC
GATAAGTCTCTTCTTTATAATGGAAAAATTATTGGAAATAATTTAATGATTGGTGTTGTT
CGATGTGAAGACGAATCAATTACAGAAAAAGAAAACATGAATTATAATCCTCAAACTTCC
ATCACTAAAATTCGTTCATTGACTCAAGCTGCATACAAGTCGGTGCGTGATGAGACGGAA
GTTGTACCAAGTGGTATCGAAGAGCCAAAAAAGACAACAGGCATAGTTAATAAAGCGATG
GATCTTATTTTTGGATGGTAAATGCAAATACTTTCATATTTTAAACAACCTTTCATTTGT
TATGTCCAATTTATATTTCTTTTTCTTAAAATAAAATAACGATATTAAAAACTTTAAAGT
TCTTATTCTTCTTAGTTGCATACGCTCTTTTCAATTCGGGACAACACTTGGAATGGAATT
GAATGGAAAAAAAATTATTTCTATTCAGTCTTTCATTGAGAGAGGATCATCTTTTGAATC
GAAATTATAA
>g10553.t2 Gene=g10553 Length=326
MEKMQLGSPQNTYLPNFLMGEQTPTNQHHRSFSNSPTASPSSMQQKFLTSLQSPNPIFNS
SMNQSFNNIHHHQQQIFQTQNPANNSAANNNNNSISGPPINSLFDNLRNEMNFQTPTKSF
YHQSIIHQDTPQPMHNNSEFNQSRILSPIPLSFPSGAVNNDFNTSTSFQNLMQQSGAIYN
NINQSMNGYSQKDFWVTVFGFPSEALTIVLSHFSGCGTILEKVCSSGNWVHLRYSSRAEC
DKSLLYNGKIIGNNLMIGVVRCEDESITEKENMNYNPQTSITKIRSLTQAAYKSVRDETE
VVPSGIEEPKKTTGIVNKAMDLIFGW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10553.t2 | CDD | cd12441 | RRM_Nup53_like | 193 | 264 | 2.14421E-29 |
| 5 | g10553.t2 | Gene3D | G3DSA:3.30.70.330 | - | 190 | 262 | 3.5E-23 |
| 8 | g10553.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 24 | 47 | - |
| 2 | g10553.t2 | PANTHER | PTHR21527 | NUCLEOPORIN NUP35 | 4 | 326 | 5.6E-35 |
| 3 | g10553.t2 | PANTHER | PTHR21527:SF6 | NUCLEOPORIN NUP35 | 4 | 326 | 5.6E-35 |
| 6 | g10553.t2 | PIRSF | PIRSF038119 | NUP53 | 1 | 326 | 3.2E-56 |
| 1 | g10553.t2 | Pfam | PF05172 | Nup53/35/40-type RNA recognition motif | 191 | 266 | 5.6E-20 |
| 9 | g10553.t2 | ProSiteProfiles | PS51472 | RNA-recognition motif (RRM) Nup35-type domain profile. | 190 | 269 | 29.289 |
| 4 | g10553.t2 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 192 | 267 | 3.59E-12 |
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 transcript has been annotated with K14313 (nuclear pore complex protein Nup53)
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.
