General information for g9877.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear RNA export factor 2.
Parent gene
- The parent gene g9877 is located on chr_1: 5869434..5872740 (+ 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 | g9877 | g9877.t1 | TSS | g9877.t1 | 5869331 | 5869331 |
| chr_1 | g9877 | g9877.t1 | isoform | g9877.t1 | 5869434 | 5872740 |
| chr_1 | g9877 | g9877.t1 | exon | g9877.t1.exon1 | 5869434 | 5869470 |
| chr_1 | g9877 | g9877.t1 | cds | g9877.t1.CDS1 | 5869434 | 5869470 |
| chr_1 | g9877 | g9877.t1 | exon | g9877.t1.exon2 | 5869525 | 5869613 |
| chr_1 | g9877 | g9877.t1 | cds | g9877.t1.CDS2 | 5869525 | 5869613 |
| chr_1 | g9877 | g9877.t1 | exon | g9877.t1.exon3 | 5869687 | 5872061 |
| chr_1 | g9877 | g9877.t1 | cds | g9877.t1.CDS3 | 5869687 | 5872061 |
| chr_1 | g9877 | g9877.t1 | exon | g9877.t1.exon4 | 5872121 | 5872219 |
| chr_1 | g9877 | g9877.t1 | cds | g9877.t1.CDS4 | 5872121 | 5872219 |
| chr_1 | g9877 | g9877.t1 | exon | g9877.t1.exon5 | 5872444 | 5872552 |
| chr_1 | g9877 | g9877.t1 | cds | g9877.t1.CDS5 | 5872444 | 5872552 |
| chr_1 | g9877 | g9877.t1 | exon | g9877.t1.exon6 | 5872615 | 5872740 |
| chr_1 | g9877 | g9877.t1 | cds | g9877.t1.CDS6 | 5872615 | 5872740 |
| chr_1 | g9877 | g9877.t1 | TTS | g9877.t1 | NA | NA |
Sequences
>g9877.t1 Gene=g9877 Length=2835
ATGGATTCAATTTTTGAGACTTTATCTCGTCATTCATCCGGGACAGTAAAAACATTTGTT
AATGAATCAAACATCAATTATCTAAAGAACTTTGCAATACCAAATCGAATCAACATGTCA
ACTGGAGAACATGCAATTATGGTGAGCTTTATGTCATCAAAAACATTCACGCCCTTAGAT
TGCTTAGGATATCAAGAATCGAATAATAATTCAAACTGGCATTTGATTTTAATCTACCAT
GAAGGTATCTTCCCAAAGGAAGATATATTAGCTGAATTATATGAAATTGCAGATGAGTCT
CTGTTTATTCCAATGGCTTATCGTAGAAATGAAAATATAGATTACTTTTTTGTATGTCAA
CAAAATGGCATGATTAAAAATTTAATTGAAAAAAACCTGCAAATTTGTGTAAAGGGATAT
ATCTTCCCTTTAGTACTTAAGATGGATGTCTCAAATCAAGTTGCAGGCCATATTAAGCCA
ATTAAGAGCATACTATCGTTAATTTTGAGAAAGATAAAAGATTCTGATTCTTCTTCACTT
GATTATTCGAATGTCAGCAGTGAAAAAGAAATGGCCGAAACTTTGATTTCATTAGGCAAT
AAAGCAACTTTGACAATGTTTTTGGACCAACTCAATCAAATTAAAACACTTAAAGCAAAC
CTTCGCGTACTCAAATTTGATAACAATAATATCAAGACACTAGAACCATTCTCTAAAAAA
CTCTATGGATTCAACGGCATAAATGTTCTTTCTCTTAATAATAATCAACTCAAAGATATT
AATGAGCTCGAGTATTTGAAGCATATGAATTTGCAAGAAATATTCATTGATGGTAATTTT
GGAGTTCATACTACAAATGCTTTCATGATCAAATATGAGAAGAAAGTTCAAAAGTTATTA
CCAACATTGAAAAGAATTAACGGTCAAACGTTGACAAATGCAGTTCATCAAGATATCAGC
TCAATAAAGAAAGAAAGCAATGAAATCTCAAATGTTGGTGATGGTGTTCTCGTGAACATT
GGAAATATAAGGCAACATCGTTGCAGAAAGCTCCAAAAAGAATATTGTTGGACAAAAGTT
ACTTTCGTTCATAACAAAAGATTTTCTGAAAGTGAAATAATGAAGCATGTGACTACAACA
CTTTTAAATGATGTTTATTTTTTCCCATGTTATTTCAAGCGAGTTGGTGATCGTGATGAA
TTCTTTTTATATAAAAACCTTGAAGCACTCGAAAAACTTTTCAATTCAGGTCTGAAAATT
CGAATGCCAACTGAGAATAATTTTATTCCGCGTAATTCCTTTCCTGTAACAATTTCTTTC
AATTTTAACGTTTCCGAATATAATGATGATGAAATATTTTGGTTTACATTGATCATTAGT
GTTTTATCAGATAGCATCAAAGAAAATGTCCTCGATCTCAATAACTTTCCTCGTAGGCCA
GAATTTCATAAAATGATTGTGCCAATGACAAAAGCATCATTAGAATTCATAATGACCCAA
GCAAAAAGACTAAATCCTAATATCACTCGTATTGATATTGAAAATTGTGATTTGACTTCT
TGTGTTGGTTTCGACTCGTGTTTATACACTTTCCCAAAGTTGACTTGCATCAATTTACGC
AATAATAAAATTTCAACTTTGCATGGATTCAAAAACTGTCCAATGATTCATGAAATATTT
TTAGATGAAAATCCGATTTGCAACCGTTCACCAAAAGATTATGTTGCTCATATAATCGAA
TATCTTCCTAACGTAAAATTCATTGATGGTCTTAAATTAAATGAGCAACGATCACTGGTG
TATTTTCAAAATTACCTTATCAAATCAAATTGCTATCCAGTCGTTAATACTTTTATAAGT
CAATTTTTTGAAACATGGGATTCATTTGAGAGAACAAAATTGGTTAAAATGTACAAAAGC
AATTCAGTCTTCACTTTTTCAATCTACTATGATAACTCGATATCAAGCAATTTAAATGTG
AGCTTTGCAAAACTTTATCCAAGAATTCAAGCATTGATCACTTTGAATAGAAATTTAAAT
AAAATTTCAAATATGAATCAAGTCATGGATAACGTTTGTATTGGTGAAAAAAATATTGAA
ATTATTTTCCAAAAACTTCCGAAAACAAAACATCATTTCCCTACTTTCACTATTGATGTA
CCACTATATGAACCTAAAAATGGAAGGATGATGATTGTTGTTGGAGGAGTATTTGAAGAT
TTCGAGAGTGAACTTTCAACAGCAACTTCAATTCCAATGGCTTTCTCTCGTACTTTTCTT
ATTTTATCAATTGATGGAGTTCTCAAAATTCAAAATGATCAAATTACAATCAATGCACCA
ACTTCAGAGCAGATAAATACAATGAAATATAATCAACAGGTAAATGAAGCTGAAGTTATA
AGTCAATGTAAGGATTTACTTCCAACTGAAGCTGAAGAGCGAGCAATGAAATTATTGATG
CTTCAAGAGTTAACTCAATGTAACAAAGAATACTGCCATAAATTATTGAGCGAAAGTTTC
TATGATTTTAAAGTTGCTTTAGCATGCTTCACAACTGCCATGGATGCAAACCAAATAACA
GATGATAAATTTGTTTTTAATCTATTTCTATTGATGTCTATTTTTGAAGCAATTCAAACG
TTTGTGTGGTTCGATGTGAATTTTATAACAAGAAGGAATCTCATAGTTACGGTCATATCT
TCATTTATATTTTTTACAGCATGGTGGATAATAATGGCAGTTTCCTTTTGTTCAGTGATA
ACTCCAACACTTTCATTTCACTTTACTGGCATTTTAAGTACTATATCATTCCTCATGGTC
AATGCCATATCATAA
>g9877.t1 Gene=g9877 Length=944
MDSIFETLSRHSSGTVKTFVNESNINYLKNFAIPNRINMSTGEHAIMVSFMSSKTFTPLD
CLGYQESNNNSNWHLILIYHEGIFPKEDILAELYEIADESLFIPMAYRRNENIDYFFVCQ
QNGMIKNLIEKNLQICVKGYIFPLVLKMDVSNQVAGHIKPIKSILSLILRKIKDSDSSSL
DYSNVSSEKEMAETLISLGNKATLTMFLDQLNQIKTLKANLRVLKFDNNNIKTLEPFSKK
LYGFNGINVLSLNNNQLKDINELEYLKHMNLQEIFIDGNFGVHTTNAFMIKYEKKVQKLL
PTLKRINGQTLTNAVHQDISSIKKESNEISNVGDGVLVNIGNIRQHRCRKLQKEYCWTKV
TFVHNKRFSESEIMKHVTTTLLNDVYFFPCYFKRVGDRDEFFLYKNLEALEKLFNSGLKI
RMPTENNFIPRNSFPVTISFNFNVSEYNDDEIFWFTLIISVLSDSIKENVLDLNNFPRRP
EFHKMIVPMTKASLEFIMTQAKRLNPNITRIDIENCDLTSCVGFDSCLYTFPKLTCINLR
NNKISTLHGFKNCPMIHEIFLDENPICNRSPKDYVAHIIEYLPNVKFIDGLKLNEQRSLV
YFQNYLIKSNCYPVVNTFISQFFETWDSFERTKLVKMYKSNSVFTFSIYYDNSISSNLNV
SFAKLYPRIQALITLNRNLNKISNMNQVMDNVCIGEKNIEIIFQKLPKTKHHFPTFTIDV
PLYEPKNGRMMIVVGGVFEDFESELSTATSIPMAFSRTFLILSIDGVLKIQNDQITINAP
TSEQINTMKYNQQVNEAEVISQCKDLLPTEAEERAMKLLMLQELTQCNKEYCHKLLSESF
YDFKVALACFTTAMDANQITDDKFVFNLFLLMSIFEAIQTFVWFDVNFITRRNLIVTVIS
SFIFFTAWWIIMAVSFCSVITPTLSFHFTGILSTISFLMVNAIS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g9877.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 161 | 316 | 2.3E-17 |
| 14 | g9877.t1 | Gene3D | G3DSA:3.80.10.10 | Ribonuclease Inhibitor | 463 | 598 | 3.8E-18 |
| 15 | g9877.t1 | Gene3D | G3DSA:3.10.450.50 | - | 601 | 801 | 8.6E-34 |
| 3 | g9877.t1 | PANTHER | PTHR10662:SF22 | NUCLEAR RNA EXPORT FACTOR 1-RELATED | 153 | 318 | 1.8E-66 |
| 5 | g9877.t1 | PANTHER | PTHR10662 | NUCLEAR RNA EXPORT FACTOR | 153 | 318 | 1.8E-66 |
| 2 | g9877.t1 | PANTHER | PTHR10662:SF22 | NUCLEAR RNA EXPORT FACTOR 1-RELATED | 467 | 865 | 1.8E-66 |
| 4 | g9877.t1 | PANTHER | PTHR10662 | NUCLEAR RNA EXPORT FACTOR | 467 | 865 | 1.8E-66 |
| 1 | g9877.t1 | Pfam | PF03943 | TAP C-terminal domain | 820 | 864 | 1.2E-4 |
| 23 | g9877.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 863 | - |
| 24 | g9877.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 864 | 886 | - |
| 21 | g9877.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 887 | 892 | - |
| 26 | g9877.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 893 | 912 | - |
| 22 | g9877.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 913 | 923 | - |
| 25 | g9877.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 924 | 943 | - |
| 20 | g9877.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 944 | 944 | - |
| 18 | g9877.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 220 | 241 | 7.504 |
| 17 | g9877.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 246 | 267 | 7.935 |
| 16 | g9877.t1 | ProSiteProfiles | PS51450 | Leucine-rich repeat profile. | 533 | 554 | 7.604 |
| 19 | g9877.t1 | ProSiteProfiles | PS50177 | Nuclear transport factor 2 domain profile. | 614 | 777 | 15.321 |
| 11 | g9877.t1 | SUPERFAMILY | SSF52058 | L domain-like | 166 | 313 | 3.97E-14 |
| 10 | g9877.t1 | SUPERFAMILY | SSF52058 | L domain-like | 466 | 596 | 1.84E-15 |
| 9 | g9877.t1 | SUPERFAMILY | SSF54427 | NTF2-like | 603 | 788 | 4.93E-27 |
| 12 | g9877.t1 | SUPERFAMILY | SSF46934 | UBA-like | 808 | 865 | 3.93E-5 |
| 7 | g9877.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 864 | 886 | - |
| 6 | g9877.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 893 | 915 | - |
| 8 | g9877.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 919 | 941 | - |
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.
