General information for g7270.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as mRNA export factor.
Parent gene
- The parent gene g7270 is located on chr_2: 22563757..22564961 (- 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 | g7270 | g7270.t3 | TTS | g7270.t3 | 22563692 | 22563692 |
| chr_2 | g7270 | g7270.t3 | isoform | g7270.t3 | 22563757 | 22564961 |
| chr_2 | g7270 | g7270.t3 | exon | g7270.t3.exon1 | 22563757 | 22564717 |
| chr_2 | g7270 | g7270.t3 | cds | g7270.t3.CDS1 | 22563918 | 22564717 |
| chr_2 | g7270 | g7270.t3 | exon | g7270.t3.exon2 | 22564781 | 22564961 |
| chr_2 | g7270 | g7270.t3 | cds | g7270.t3.CDS2 | 22564781 | 22564961 |
| chr_2 | g7270 | g7270.t3 | TSS | g7270.t3 | 22565173 | 22565173 |
Sequences
>g7270.t3 Gene=g7270 Length=1142
ATGTTTTCGCAGAGTAATGTAATAAATCAATCGAATCCTATGAAGGATATCGAAGTAACA
TCTCCTCCAGATGATACAATATCTGCATTGAAATTCTCACCACAAACAATTTTACCTAAA
AATTTTCTTCTTGCTGGAAGTTGGGATTGTTCTGTAAGATGTTGGGAAGTTGCTGATACA
GGATTAACAACTCCCAAAGCAATGAAAACAATGACTGCACCAGTACTTGATGTTTGTTGG
CATGATGATGGTACAAAAGCATTTTTTGCAGGCGCTGATAAAACTGCAAGAGCGTGGGAT
TTAGCAGCTGATCAAGTCATGCAAGTTGCAGCACATGATAACACAGTCAAGACATGCCAT
TGGATTAAAGCTCCAAATTACACTTGCTTAATGACAGGTAGTTGGGATAAAACACTTAAA
TTCTGGGATTTGAGACAACAAAATCCTATTTTACAACTACAATTACCTGAAAGATGTTAT
ACAGCAGATGTAGAATACCCAATGGCAGTAGTTGGCACAGCAAATCGCCATATAATTATT
TACTCACTAGATAATCAACCTACTGAATTCAAACGATATGAAAGTCCATTAAAATATCAA
CATCGCTGTGTGTCAGTGTTTAGTGATATGAAAAAGAAACAGCCAGTTGGTTATGCTCTC
GGTTCTATTGAAGGTCGAGTTGCTATTCAATATTTGAATCCTCAGAATCCCAAAGATAAT
TTCACATTTAAATGTCATCGTGTAAATGGAGCATCAAATTTTCAAGATATTTATGCAGTT
AATGATATTGCTTTCCATCCAATTCATGGAACATTAGCAACAGTAGGATCAGATGGAACT
TTCAGTTTTTGGGATAAAGACGCAAGAACGAAACTAAAGAGTTCTGAGACAATCGATCAG
TCAATAACAAAATGCGCTTTCTCAGCTGGCGGACAGATTTTCGCATATGCAGTCGGTTAC
GATTGGTCAAAGGTAAATTAAAACACATAGTCAACAAGTGGCTGCCATAAAATAATTTTT
CACACATTTACCCACTTTTCATCTCATTCCAGGGTCACGAGTTTTACAATCCTCAAAAGA
AAAGTTATATTTTATTAAGATCATGCTTTGAAGAACTCAAACCTCGTGTACACAATTCTT
AA
>g7270.t3 Gene=g7270 Length=326
MFSQSNVINQSNPMKDIEVTSPPDDTISALKFSPQTILPKNFLLAGSWDCSVRCWEVADT
GLTTPKAMKTMTAPVLDVCWHDDGTKAFFAGADKTARAWDLAADQVMQVAAHDNTVKTCH
WIKAPNYTCLMTGSWDKTLKFWDLRQQNPILQLQLPERCYTADVEYPMAVVGTANRHIII
YSLDNQPTEFKRYESPLKYQHRCVSVFSDMKKKQPVGYALGSIEGRVAIQYLNPQNPKDN
FTFKCHRVNGASNFQDIYAVNDIAFHPIHGTLATVGSDGTFSFWDKDARTKLKSSETIDQ
SITKCAFSAGGQIFAYAVGYDWSKVN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g7270.t3 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 326 | 1.2E-108 |
| 4 | g7270.t3 | PANTHER | PTHR10971 | MRNA EXPORT FACTOR AND BUB3 | 8 | 324 | 3.6E-134 |
| 5 | g7270.t3 | PANTHER | PTHR10971:SF11 | MRNA EXPORT FACTOR | 8 | 324 | 3.6E-134 |
| 8 | g7270.t3 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 43 | 57 | 6.4E-6 |
| 7 | g7270.t3 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 130 | 144 | 6.4E-6 |
| 6 | g7270.t3 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 272 | 286 | 6.4E-6 |
| 2 | g7270.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 27 | 55 | 0.024 |
| 3 | g7270.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 111 | 143 | 0.0041 |
| 1 | g7270.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 242 | 285 | 0.031 |
| 11 | g7270.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 130 | 144 | - |
| 16 | g7270.t3 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 20 | 152 | 16.269 |
| 17 | g7270.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 68 | 109 | 9.205 |
| 19 | g7270.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 109 | 152 | 9.673 |
| 18 | g7270.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 260 | 294 | 8.938 |
| 13 | g7270.t3 | SMART | SM00320 | WD40_4 | 13 | 56 | 0.71 |
| 12 | g7270.t3 | SMART | SM00320 | WD40_4 | 64 | 100 | 0.015 |
| 15 | g7270.t3 | SMART | SM00320 | WD40_4 | 102 | 143 | 0.013 |
| 14 | g7270.t3 | SMART | SM00320 | WD40_4 | 236 | 285 | 9.3E-4 |
| 9 | g7270.t3 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 18 | 322 | 1.3E-46 |
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:0006406 | mRNA export from nucleus | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14298 (mRNA 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.
