General information for g7270.t2
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.t2 | TTS | g7270.t2 | 22563692 | 22563692 |
| chr_2 | g7270 | g7270.t2 | isoform | g7270.t2 | 22563757 | 22564961 |
| chr_2 | g7270 | g7270.t2 | exon | g7270.t2.exon1 | 22563757 | 22563846 |
| chr_2 | g7270 | g7270.t2 | cds | g7270.t2.CDS1 | 22563757 | 22563846 |
| chr_2 | g7270 | g7270.t2 | exon | g7270.t2.exon2 | 22563927 | 22564961 |
| chr_2 | g7270 | g7270.t2 | cds | g7270.t2.CDS2 | 22563927 | 22564697 |
| chr_2 | g7270 | g7270.t2 | TSS | g7270.t2 | 22565173 | 22565173 |
Sequences
>g7270.t2 Gene=g7270 Length=1125
ATGTTTTCGCAGAGTAATGTAATAAATCAATCGAATCCTATGAAGGATATCGAAGTAACA
TCTCCTCCAGATGATACAATATCTGCATTGAAATTCTCACCACAAACAATTTTACCTAAA
AATTTTCTTCTTGCTGGAAGTTGGGATTGTTCTGTAAGATGTTGGGAAGTTGCTGATACA
GGTATATTGAGATGAATTCTTTAATGATCAGTTAATGTTTTAATAATAAATTTGTATATT
TTAGGATTAACAACTCCCAAAGCAATGAAAACAATGACTGCACCAGTACTTGATGTTTGT
TGGCATGATGATGGTACAAAAGCATTTTTTGCAGGCGCTGATAAAACTGCAAGAGCGTGG
GATTTAGCAGCTGATCAAGTCATGCAAGTTGCAGCACATGATAACACAGTCAAGACATGC
CATTGGATTAAAGCTCCAAATTACACTTGCTTAATGACAGGTAGTTGGGATAAAACACTT
AAATTCTGGGATTTGAGACAACAAAATCCTATTTTACAACTACAATTACCTGAAAGATGT
TATACAGCAGATGTAGAATACCCAATGGCAGTAGTTGGCACAGCAAATCGCCATATAATT
ATTTACTCACTAGATAATCAACCTACTGAATTCAAACGATATGAAAGTCCATTAAAATAT
CAACATCGCTGTGTGTCAGTGTTTAGTGATATGAAAAAGAAACAGCCAGTTGGTTATGCT
CTCGGTTCTATTGAAGGTCGAGTTGCTATTCAATATTTGAATCCTCAGAATCCCAAAGAT
AATTTCACATTTAAATGTCATCGTGTAAATGGAGCATCAAATTTTCAAGATATTTATGCA
GTTAATGATATTGCTTTCCATCCAATTCATGGAACATTAGCAACAGTAGGATCAGATGGA
ACTTTCAGTTTTTGGGATAAAGACGCAAGAACGAAACTAAAGAGTTCTGAGACAATCGAT
CAGTCAATAACAAAATGCGCTTTCTCAGCTGGCGGACAGATTTTCGCATATGCAGTCGGT
TACGATTGGTCAAAGGGTCACGAGTTTTACAATCCTCAAAAGAAAAGTTATATTTTATTA
AGATCATGCTTTGAAGAACTCAAACCTCGTGTACACAATTCTTAA
>g7270.t2 Gene=g7270 Length=286
MKTMTAPVLDVCWHDDGTKAFFAGADKTARAWDLAADQVMQVAAHDNTVKTCHWIKAPNY
TCLMTGSWDKTLKFWDLRQQNPILQLQLPERCYTADVEYPMAVVGTANRHIIIYSLDNQP
TEFKRYESPLKYQHRCVSVFSDMKKKQPVGYALGSIEGRVAIQYLNPQNPKDNFTFKCHR
VNGASNFQDIYAVNDIAFHPIHGTLATVGSDGTFSFWDKDARTKLKSSETIDQSITKCAF
SAGGQIFAYAVGYDWSKGHEFYNPQKKSYILLRSCFEELKPRVHNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g7270.t2 | Gene3D | G3DSA:2.130.10.10 | - | 1 | 285 | 7.1E-95 |
| 3 | g7270.t2 | PANTHER | PTHR10971 | MRNA EXPORT FACTOR AND BUB3 | 4 | 281 | 3.7E-115 |
| 4 | g7270.t2 | PANTHER | PTHR10971:SF11 | MRNA EXPORT FACTOR | 4 | 281 | 3.7E-115 |
| 6 | g7270.t2 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 20 | 34 | 8.4E-5 |
| 5 | g7270.t2 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 63 | 77 | 8.4E-5 |
| 7 | g7270.t2 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 205 | 219 | 8.4E-5 |
| 2 | g7270.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 44 | 76 | 0.0034 |
| 1 | g7270.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 175 | 218 | 0.026 |
| 10 | g7270.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 63 | 77 | - |
| 14 | g7270.t2 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 1 | 85 | 12.526 |
| 16 | g7270.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 1 | 42 | 9.205 |
| 17 | g7270.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 42 | 85 | 9.673 |
| 15 | g7270.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 193 | 227 | 8.938 |
| 13 | g7270.t2 | SMART | SM00320 | WD40_4 | 1 | 33 | 27.0 |
| 11 | g7270.t2 | SMART | SM00320 | WD40_4 | 35 | 76 | 0.013 |
| 12 | g7270.t2 | SMART | SM00320 | WD40_4 | 169 | 218 | 9.3E-4 |
| 8 | g7270.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 5 | 253 | 3.25E-37 |
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.
