General information for g9996.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nucleoporin Nup37.
Parent gene
- The parent gene g9996 is located on chr_1: 6485181..6485634 (- 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 | g9996 | g9996.t1 | TTS | g9996.t1 | 6483762 | 6483762 |
| chr_1 | g9996 | g9996.t1 | isoform | g9996.t1 | 6484629 | 6485634 |
| chr_1 | g9996 | g9996.t1 | exon | g9996.t1.exon1 | 6484629 | 6484881 |
| chr_1 | g9996 | g9996.t1 | cds | g9996.t1.CDS1 | 6484629 | 6484881 |
| chr_1 | g9996 | g9996.t1 | exon | g9996.t1.exon2 | 6484943 | 6485634 |
| chr_1 | g9996 | g9996.t1 | cds | g9996.t1.CDS2 | 6484943 | 6485634 |
| chr_1 | g9996 | g9996.t1 | TSS | g9996.t1 | 6485682 | 6485682 |
Sequences
>g9996.t1 Gene=g9996 Length=945
ATGCAAAATATATCGCATCAAGCAAGACCGACATTTGAAATTGATATAAATGATAAGATA
GTGTGCTACGAATCATCACAACCATTAATACATGGTGAAAGTGTTTTATTAATTGCATTA
AAAACGAGAATTTCTATTTTGGCGCTTGATATTGGGACGGAAGATTTCACTCTCGATTAT
AGAACAATTAAAGATATAGCTGAGCCAGATATAAGACTGCTTAAACTTTGTTCTCAAGCA
ATCGCAAGGAATATTTTGTTTGCAGCATGTCCTTCAAAGTACACAATTAAAATATTTTCT
GTTAATGAGAGTGAAGTTATATGTCTCAACAAAATTGCAGCTCATAGCAATTATATAAAT
TCAATAGATTTTTCTGAGGAATATTTAGCATCTGGGAGTGATGATCACACATGCAAAATC
TATTCTGTTAAAGAAAACTATTCCGAACATTCCGTTTTGAATTTCTCAGCATCTGTAACT
TGTGTGAAGTTTAATCCTGAAGAGCCTAATAAGCTTTTAATCAGCGTTAAAAATGGCAAT
TTATTCATCTATTGTCTGAAACTCAAGCAATCGCTTTATAGTTTCTATACTCATTCACCA
TTAATGCATTTTGACTGGTCTTTAAAGAATCCAAGTATTGTGGCTGCAATTGCTTACGAT
CAAGTTTTTTATTTTGACATCTCGAAACCAGATGTGCCAATCTACAGCAAAAGATTAAGT
GATGTTGGTAAAATAATTACAATTCATCCATCAAATCCTCTTATATCAGCAGTTGTTTGT
AATAGAGCATCAACAGAAATCAAAGTCATTCATCAAAAGAGTACTATTTCGAATATATTT
TCAACGAAAATTATATCATACGCTGGAAATATTACGTGGAATTCATCTTATTTAATCGTT
GGATCTGATCGAAAAATTTGTTTCTATAAGATACCAATTGCATAA
>g9996.t1 Gene=g9996 Length=314
MQNISHQARPTFEIDINDKIVCYESSQPLIHGESVLLIALKTRISILALDIGTEDFTLDY
RTIKDIAEPDIRLLKLCSQAIARNILFAACPSKYTIKIFSVNESEVICLNKIAAHSNYIN
SIDFSEEYLASGSDDHTCKIYSVKENYSEHSVLNFSASVTCVKFNPEEPNKLLISVKNGN
LFIYCLKLKQSLYSFYTHSPLMHFDWSLKNPSIVAAIAYDQVFYFDISKPDVPIYSKRLS
DVGKIITIHPSNPLISAVVCNRASTEIKVIHQKSTISNIFSTKIISYAGNITWNSSYLIV
GSDRKICFYKIPIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9996.t1 | Gene3D | G3DSA:2.130.10.10 | - | 11 | 311 | 0.0000e+00 |
| 2 | g9996.t1 | PANTHER | PTHR22806 | NUCLEOPORIN NUP37 P37 -RELATED | 7 | 311 | 0.0000e+00 |
| 1 | g9996.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 108 | 141 | 3.3000e-04 |
| 8 | g9996.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 112 | 194 | 1.1972e+01 |
| 9 | g9996.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 112 | 151 | 1.0174e+01 |
| 6 | g9996.t1 | SMART | SM00320 | WD40_4 | 105 | 142 | 9.1000e-06 |
| 5 | g9996.t1 | SMART | SM00320 | WD40_4 | 146 | 185 | 1.6000e+00 |
| 4 | g9996.t1 | SMART | SM00320 | WD40_4 | 188 | 226 | 3.5000e+02 |
| 3 | g9996.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 83 | 311 | 0.0000e+00 |
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:0005515 | protein binding | MF |
| GO:0031080 | nuclear pore outer ring | CC |
KEGG
Orthology
- This transcript has been annotated with K14302 (nuclear pore complex protein Nup37)
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.
