General information for g7117.t3
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.t3 | TSS | g7117.t3 | 21268115 | 21268115 |
| chr_2 | g7117 | g7117.t3 | isoform | g7117.t3 | 21268194 | 21270570 |
| chr_2 | g7117 | g7117.t3 | exon | g7117.t3.exon1 | 21268194 | 21268257 |
| chr_2 | g7117 | g7117.t3 | exon | g7117.t3.exon2 | 21268856 | 21268951 |
| chr_2 | g7117 | g7117.t3 | exon | g7117.t3.exon3 | 21269007 | 21269290 |
| chr_2 | g7117 | g7117.t3 | exon | g7117.t3.exon4 | 21269354 | 21270570 |
| chr_2 | g7117 | g7117.t3 | cds | g7117.t3.CDS1 | 21269455 | 21270570 |
| chr_2 | g7117 | g7117.t3 | TTS | g7117.t3 | 21270622 | 21270622 |
Sequences
>g7117.t3 Gene=g7117 Length=1661
ATGTCTTTTAACTTTGGAAATACAAGCACAACAGGATTAGGAGGCACAAGCACTCCGGCA
AAACCTTTGCTACACCAGCCACTTCTGCGCCTCCATTCGGAACAAACACAAGTACTTTCG
GCACACCAGCGTCATCAGTACCTACATTTGGTCAAACTAACACGAGTTCATTTTCATTTG
GTGGTGCTCAAACAACAACATCTGCACCAACGTTTGGTTTTGGAAGTTCAGTAACTACCA
CAAGTGCACCCTCAGCTTTCAATTTTGGTGCTACAAATACTTCTCAACCCTCTGCTTTTA
GTTTTGGACAAACAGCTACTAGTCAGGCTCCAGCGTTTAATTTTGGAGGAGGAACTTCAA
CTTCTCAAGCTCCTTCATTATTCGGAACTAGCAATACGAGTACTTTTGGAGGAGGAACAG
CTTTTGGACAAACTGGATTTAGTGGATTTGGTCAACAAAATCAACAACAACAAACTACAC
TTTTGCCTGAGGAATTATTTCAACAAGCAATTTTTAATGTTTCCATCTATGGTGATGAGC
GCGATATGGTTCTTGCTAAATGGAATTATTTGCAAGCTCGATTTGGCATAGGAAAAGCTA
TGTATTCACAATCGCAACCACCTGTTGATATTACACCACAAAATTATTTGTGTAGTTTCA
AAGCAATGGGATATAGTCGGCTTCCTGGAAAAGATAATAAACTGGGTCTGGTTGCGCTCA
AATTCAATAGACCGTTGTCACAAATGAAAGATCAAGAACAGCAACTCATTCCAAAATTAA
GTCAGATTTTTGGAAGCAAACCAAATTTGATAATTCATATTGAGTCAATGAAATCACTTT
CTGATGTTGCAACTCAGGTCATCATGTATGTAGAAGAAAAACTGCCAAACTCTACTGAAA
CGAAACGTTTTCCAGCGACTGAAACAAACAGTTTTTTAAATCAAGGCCATTTAAAATTTC
AATTGCAGCAAATGGGAGTTGAAGAAATTTATCCGATGATTCCACCGGATGCTGATCAGT
TAAAACAATATCTCTCTACACCACCAAAGGGAATTGACTTTCGTATGTGGCAACAAGCGA
TTAATGATAATCCCGATGCGAAAAATTTCATACCCGTTCCATTAATTTGCTTCAGCGATC
TTAAGTCACGCCTGGCATGTCAAGAAAATGAAACATCAAATCATATGAACTATCTTTCAA
AATTAGAAAAAGATATTAATGAATTGAAATTGCGTCACACAAGCACCACAACAAAAATCA
CTGAACAGCGAAGAAAATTAGCGGAATTGAGTCATCGTATATTGAGGATTATTGTAAAGC
AAGAATCAACAAGAAAAGCTGGTCTCGCTCTTACGCCAGAAGAGGAAACAATAAAAACAG
TTTTGGAAAACATGCATGCACTAGTATCAGCTCCAACACAATTCAAAGGTAAATTAAATG
AATTGCTTGCTCAAATGCGTATGCAAAGAAGCCAATGGGCAGCATGTGGTACAAGTGAAT
ATAGTTTGGATAAAGATTCATCTGATGAAATGAAAAATTTCCTCACTATGCAACAAAAGA
CCATGGAACTGCTAATTGAAACAATCAACAAAGATTTAAAAGATTTGAAAACTATCAGTG
AAGGTATGAGTCGTATGCATAGTGGTAGTGTTATAAATTAA
>g7117.t3 Gene=g7117 Length=371
MVLAKWNYLQARFGIGKAMYSQSQPPVDITPQNYLCSFKAMGYSRLPGKDNKLGLVALKF
NRPLSQMKDQEQQLIPKLSQIFGSKPNLIIHIESMKSLSDVATQVIMYVEEKLPNSTETK
RFPATETNSFLNQGHLKFQLQQMGVEEIYPMIPPDADQLKQYLSTPPKGIDFRMWQQAIN
DNPDAKNFIPVPLICFSDLKSRLACQENETSNHMNYLSKLEKDINELKLRHTSTTTKITE
QRRKLAELSHRILRIIVKQESTRKAGLALTPEEETIKTVLENMHALVSAPTQFKGKLNEL
LAQMRMQRSQWAACGTSEYSLDKDSSDEMKNFLTMQQKTMELLIETINKDLKDLKTISEG
MSRMHSGSVIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g7117.t3 | Coils | Coil | Coil | 217 | 237 | - |
| 5 | g7117.t3 | Gene3D | G3DSA:1.20.5.490 | Single helix bin | 206 | 270 | 3.0E-22 |
| 3 | g7117.t3 | PANTHER | PTHR13000:SF0 | NUCLEOPORIN P54 | 2 | 363 | 8.9E-68 |
| 4 | g7117.t3 | PANTHER | PTHR13000 | NUCLEOPORIN P54 | 2 | 363 | 8.9E-68 |
| 1 | g7117.t3 | Pfam | PF13874 | Nucleoporin complex subunit 54 | 166 | 304 | 1.7E-38 |
| 2 | g7117.t3 | Pfam | PF18437 | Nup54 C-terminal interacting domain | 319 | 357 | 5.3E-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.
