General information for g7117.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Probable nucleoporin Nup54.
Parent gene
- The parent gene g7117 is located on chr_2: 21270570..21271967 (+ 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_2 | g7117 | g7117.t1 | TSS | g7117.t1 | 21268115 | 21268115 |
| chr_2 | g7117 | g7117.t1 | isoform | g7117.t1 | 21268194 | 21270570 |
| chr_2 | g7117 | g7117.t1 | exon | g7117.t1.exon1 | 21268194 | 21268257 |
| chr_2 | g7117 | g7117.t1 | cds | g7117.t1.CDS1 | 21268194 | 21268257 |
| chr_2 | g7117 | g7117.t1 | exon | g7117.t1.exon2 | 21268840 | 21268951 |
| chr_2 | g7117 | g7117.t1 | cds | g7117.t1.CDS2 | 21268840 | 21268951 |
| chr_2 | g7117 | g7117.t1 | exon | g7117.t1.exon3 | 21269007 | 21269290 |
| chr_2 | g7117 | g7117.t1 | cds | g7117.t1.CDS3 | 21269007 | 21269290 |
| chr_2 | g7117 | g7117.t1 | exon | g7117.t1.exon4 | 21269354 | 21270570 |
| chr_2 | g7117 | g7117.t1 | cds | g7117.t1.CDS4 | 21269354 | 21270570 |
| chr_2 | g7117 | g7117.t1 | TTS | g7117.t1 | 21270622 | 21270622 |
Sequences
>g7117.t1 Gene=g7117 Length=1677
ATGTCTTTTAACTTTGGAAATACAAGCACAACAGGATTAGGAGGCACAAGCACTCCGGCA
AAACCTGCCTTTGGTTTTAGCTTTGCTACACCAGCCACTTCTGCGCCTCCATTCGGAACA
AACACAAGTACTTTCGGCACACCAGCGTCATCAGTACCTACATTTGGTCAAACTAACACG
AGTTCATTTTCATTTGGTGGTGCTCAAACAACAACATCTGCACCAACGTTTGGTTTTGGA
AGTTCAGTAACTACCACAAGTGCACCCTCAGCTTTCAATTTTGGTGCTACAAATACTTCT
CAACCCTCTGCTTTTAGTTTTGGACAAACAGCTACTAGTCAGGCTCCAGCGTTTAATTTT
GGAGGAGGAACTTCAACTTCTCAAGCTCCTTCATTATTCGGAACTAGCAATACGAGTACT
TTTGGAGGAGGAACAGCTTTTGGACAAACTGGATTTAGTGGATTTGGTCAACAAAATCAA
CAACAACAAACTACACTTTTGCCTGAGGAATTATTTCAACAAGCAATTTTTAATGTTTCC
ATCTATGGTGATGAGCGCGATATGGTTCTTGCTAAATGGAATTATTTGCAAGCTCGATTT
GGCATAGGAAAAGCTATGTATTCACAATCGCAACCACCTGTTGATATTACACCACAAAAT
TATTTGTGTAGTTTCAAAGCAATGGGATATAGTCGGCTTCCTGGAAAAGATAATAAACTG
GGTCTGGTTGCGCTCAAATTCAATAGACCGTTGTCACAAATGAAAGATCAAGAACAGCAA
CTCATTCCAAAATTAAGTCAGATTTTTGGAAGCAAACCAAATTTGATAATTCATATTGAG
TCAATGAAATCACTTTCTGATGTTGCAACTCAGGTCATCATGTATGTAGAAGAAAAACTG
CCAAACTCTACTGAAACGAAACGTTTTCCAGCGACTGAAACAAACAGTTTTTTAAATCAA
GGCCATTTAAAATTTCAATTGCAGCAAATGGGAGTTGAAGAAATTTATCCGATGATTCCA
CCGGATGCTGATCAGTTAAAACAATATCTCTCTACACCACCAAAGGGAATTGACTTTCGT
ATGTGGCAACAAGCGATTAATGATAATCCCGATGCGAAAAATTTCATACCCGTTCCATTA
ATTTGCTTCAGCGATCTTAAGTCACGCCTGGCATGTCAAGAAAATGAAACATCAAATCAT
ATGAACTATCTTTCAAAATTAGAAAAAGATATTAATGAATTGAAATTGCGTCACACAAGC
ACCACAACAAAAATCACTGAACAGCGAAGAAAATTAGCGGAATTGAGTCATCGTATATTG
AGGATTATTGTAAAGCAAGAATCAACAAGAAAAGCTGGTCTCGCTCTTACGCCAGAAGAG
GAAACAATAAAAACAGTTTTGGAAAACATGCATGCACTAGTATCAGCTCCAACACAATTC
AAAGGTAAATTAAATGAATTGCTTGCTCAAATGCGTATGCAAAGAAGCCAATGGGCAGCA
TGTGGTACAAGTGAATATAGTTTGGATAAAGATTCATCTGATGAAATGAAAAATTTCCTC
ACTATGCAACAAAAGACCATGGAACTGCTAATTGAAACAATCAACAAAGATTTAAAAGAT
TTGAAAACTATCAGTGAAGGTATGAGTCGTATGCATAGTGGTAGTGTTATAAATTAA
>g7117.t1 Gene=g7117 Length=558
MSFNFGNTSTTGLGGTSTPAKPAFGFSFATPATSAPPFGTNTSTFGTPASSVPTFGQTNT
SSFSFGGAQTTTSAPTFGFGSSVTTTSAPSAFNFGATNTSQPSAFSFGQTATSQAPAFNF
GGGTSTSQAPSLFGTSNTSTFGGGTAFGQTGFSGFGQQNQQQQTTLLPEELFQQAIFNVS
IYGDERDMVLAKWNYLQARFGIGKAMYSQSQPPVDITPQNYLCSFKAMGYSRLPGKDNKL
GLVALKFNRPLSQMKDQEQQLIPKLSQIFGSKPNLIIHIESMKSLSDVATQVIMYVEEKL
PNSTETKRFPATETNSFLNQGHLKFQLQQMGVEEIYPMIPPDADQLKQYLSTPPKGIDFR
MWQQAINDNPDAKNFIPVPLICFSDLKSRLACQENETSNHMNYLSKLEKDINELKLRHTS
TTTKITEQRRKLAELSHRILRIIVKQESTRKAGLALTPEEETIKTVLENMHALVSAPTQF
KGKLNELLAQMRMQRSQWAACGTSEYSLDKDSSDEMKNFLTMQQKTMELLIETINKDLKD
LKTISEGMSRMHSGSVIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7117.t1 | Coils | Coil | Coil | 404 | 424 | - |
| 5 | g7117.t1 | Gene3D | G3DSA:1.20.5.490 | Single helix bin | 393 | 457 | 5.4E-22 |
| 3 | g7117.t1 | PANTHER | PTHR13000:SF0 | NUCLEOPORIN P54 | 1 | 550 | 3.2E-96 |
| 4 | g7117.t1 | PANTHER | PTHR13000 | NUCLEOPORIN P54 | 1 | 550 | 3.2E-96 |
| 1 | g7117.t1 | Pfam | PF13874 | Nucleoporin complex subunit 54 | 353 | 491 | 3.8E-38 |
| 2 | g7117.t1 | Pfam | PF18437 | Nup54 C-terminal interacting domain | 506 | 544 | 9.1E-13 |
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:0005643 | nuclear pore | CC |
KEGG
Orthology
- This transcript has been annotated with K14308 (nuclear pore complex protein Nup54)
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.
