General information for g1194.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Nuclear RNA export factor 1.
Parent gene
- The parent gene g1194 is located on chr_3: 8695727..8698054 (+ 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_3 | g1194 | g1194.t1 | TSS | g1194.t1 | 8693701 | 8693701 |
| chr_3 | g1194 | g1194.t1 | isoform | g1194.t1 | 8693914 | 8695727 |
| chr_3 | g1194 | g1194.t1 | exon | g1194.t1.exon1 | 8693914 | 8694444 |
| chr_3 | g1194 | g1194.t1 | cds | g1194.t1.CDS1 | 8693914 | 8694444 |
| chr_3 | g1194 | g1194.t1 | exon | g1194.t1.exon2 | 8694510 | 8694619 |
| chr_3 | g1194 | g1194.t1 | cds | g1194.t1.CDS2 | 8694510 | 8694619 |
| chr_3 | g1194 | g1194.t1 | exon | g1194.t1.exon3 | 8694682 | 8694718 |
| chr_3 | g1194 | g1194.t1 | cds | g1194.t1.CDS3 | 8694682 | 8694718 |
| chr_3 | g1194 | g1194.t1 | exon | g1194.t1.exon4 | 8694773 | 8695014 |
| chr_3 | g1194 | g1194.t1 | cds | g1194.t1.CDS4 | 8694773 | 8695014 |
| chr_3 | g1194 | g1194.t1 | exon | g1194.t1.exon5 | 8695070 | 8695241 |
| chr_3 | g1194 | g1194.t1 | cds | g1194.t1.CDS5 | 8695070 | 8695241 |
| chr_3 | g1194 | g1194.t1 | exon | g1194.t1.exon6 | 8695299 | 8695727 |
| chr_3 | g1194 | g1194.t1 | cds | g1194.t1.CDS6 | 8695299 | 8695727 |
| chr_3 | g1194 | g1194.t1 | TTS | g1194.t1 | 8695827 | 8695827 |
Sequences
>g1194.t1 Gene=g1194 Length=1521
ATGGAAAGACAAAATCAAAAATTCAAACATCACAATCAAAAGAAAACTGGACATTTCAGA
AAGCAAAAGAATCCACAAAAAAGAAAATCTACTCTAACTACTAATTCAAATCACAATTTA
TTTCGTCGTAATGAAAACTTCAAAAACTTTCAATCTAAAGCTCGTGATTTAGCTAACAAT
ATTAAAAAGAGGAGATTATTAAACCTTCCAAATATCATCAGTCATACAAGTTCAATTAAG
GTAACTGAAGAAGAAAAAGAAAAAATGAAGAATGCAATGGTGAATAGATACAACTTTCAA
ACGAAAGCGCTTGATTTAACAAATTTCGGAAAGAATGATGATTTAATTGATTTCAAGTGT
GAGCTTTTTCGGCAACCATACCTTTGCGCTGCTATTGACATAATTGTAAATTATATTCCT
GATCTTGAAGCTCTAAATTTAAATGAAAATAATCTCAACCTTATTGGTCGTCTGGGAAGT
TTTACAAACAAATTACCTAATTTAAAAATACTTTATCTCGCGAAAAATAATATTGCAATG
CACAGTTCACTTAATATTTTAAAGAATTTGCCGTTAGTTGAACTTTCTTTGGAAGGAAAT
CCATTTATTAAAGATTTCAAGAACAAAAATGAATATGTCGCTGAAATAAGAAAAACATTT
CCAAAACTTTTAAAATTGGATGGAAAATTTTTGGATCCCGTGATAAATTTTGATTTAGTT
GAAGAAAGAAAAGCATTACCATCATGGAAAAAGTTATATCTCTGCAATCCTTCTGGTCAA
GAAATTGTAACAAAATTTATTCAACAATATTTTTCGATTTACGATTCTGATAATCGACAG
CATTTGCTTGATGCTTATCATGATAACGCATTATTTTCAATAACTGCCACTTATATTCAA
AGTCCAGCTCAAAGAGAAATTCTAACTTCATATCAAAGAATCGGTAGGAATTTACTACGA
AAGAGTTTGACATCTGAAATCCGTCTGAGCAGTCTTAAAAGAGGAAAAGTTTCAGTAGTT
GCGTTATTAAACGATCTACCTCCAACAAAACATGATCCTCAATCGTTTGCAGTTGATCTG
ACTTTCTTTACTCAACAAATGATTGTTCTCACTATTACTGGCATCTTCAAAGAAAAAAAA
TCTGATCCTAAAGCCGAATATGTGAGAGTGTTTCAGAAGACTCTCATTATTGTGCCAAAT
TCAGTAGGTGGCTTGTGCATTAGAAATGAAATGATGCATATCAATAATGCAACTTTAACT
CAATCAAAGAAAGCTTTCAAAACTTTAATAATTCCAAAACCATTGTCAGCGACAATTTCT
TCTCAGGCTGAACTTCAAGATGAAGAAAACACAAAGATCAAAATGGTACAAGCATTAAGC
AAGCAAACAAATATGAATTTAGAATGGAGCAAAAAGTGTTTGGAAGAGACAAATTATGAT
TATAATCGTGCCTGTTTTGTATTTAATGAACTTTATAAGATAAACAAGATTCCACAAGAG
GCTTTCTCAATGTTGGAATAA
>g1194.t1 Gene=g1194 Length=506
MERQNQKFKHHNQKKTGHFRKQKNPQKRKSTLTTNSNHNLFRRNENFKNFQSKARDLANN
IKKRRLLNLPNIISHTSSIKVTEEEKEKMKNAMVNRYNFQTKALDLTNFGKNDDLIDFKC
ELFRQPYLCAAIDIIVNYIPDLEALNLNENNLNLIGRLGSFTNKLPNLKILYLAKNNIAM
HSSLNILKNLPLVELSLEGNPFIKDFKNKNEYVAEIRKTFPKLLKLDGKFLDPVINFDLV
EERKALPSWKKLYLCNPSGQEIVTKFIQQYFSIYDSDNRQHLLDAYHDNALFSITATYIQ
SPAQREILTSYQRIGRNLLRKSLTSEIRLSSLKRGKVSVVALLNDLPPTKHDPQSFAVDL
TFFTQQMIVLTITGIFKEKKSDPKAEYVRVFQKTLIIVPNSVGGLCIRNEMMHINNATLT
QSKKAFKTLIIPKPLSATISSQAELQDEENTKIKMVQALSKQTNMNLEWSKKCLEETNYD
YNRACFVFNELYKINKIPQEAFSMLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g1194.t1 | CDD | cd14342 | UBA_TAP-C | 455 | 502 | 3.39815E-21 |
| 7 | g1194.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 80 | 237 | 2.2E-32 |
| 9 | g1194.t1 | Gene3D | G3DSA:3.10.450.50 | - | 248 | 431 | 4.3E-52 |
| 8 | g1194.t1 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 448 | 503 | 7.5E-22 |
| 13 | g1194.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 35 | - |
| 12 | g1194.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 8 | 27 | - |
| 3 | g1194.t1 | PANTHER | PTHR10662 | NUCLEAR RNA EXPORT FACTOR | 77 | 502 | 2.6E-105 |
| 2 | g1194.t1 | Pfam | PF02136 | Nuclear transport factor 2 (NTF2) domain | 262 | 412 | 6.7E-7 |
| 1 | g1194.t1 | Pfam | PF03943 | TAP C-terminal domain | 455 | 502 | 6.5E-22 |
| 15 | g1194.t1 | ProSiteProfiles | PS50177 | Nuclear transport factor 2 domain profile. | 262 | 414 | 19.873 |
| 14 | g1194.t1 | ProSiteProfiles | PS51281 | TAP C-terminal (TAP-C) domain profile. | 450 | 505 | 25.39 |
| 11 | g1194.t1 | SMART | SM00804 | TAP_C_cls | 441 | 504 | 4.2E-20 |
| 5 | g1194.t1 | SUPERFAMILY | SSF52058 | L domain-like | 82 | 231 | 7.82E-23 |
| 4 | g1194.t1 | SUPERFAMILY | SSF54427 | NTF2-like | 247 | 427 | 1.31E-42 |
| 6 | g1194.t1 | SUPERFAMILY | SSF46934 | UBA-like | 449 | 502 | 2.84E-19 |
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:0005634 | nucleus | CC |
| GO:0005515 | protein binding | MF |
| GO:0051028 | mRNA transport | BP |
KEGG
Orthology
- This transcript has been annotated with K14284 (nuclear RNA export factor)
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.
