General information for g5798.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Eukaryotic translation initiation factor 3 subunit H.
Parent gene
- The parent gene g5798 is located on chr_2: 11983809..11984764 (+ 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 | g5798 | g5798.t1 | TSS | g5798.t1 | 11983529 | 11983529 |
| chr_2 | g5798 | g5798.t1 | isoform | g5798.t1 | 11983605 | 11984710 |
| chr_2 | g5798 | g5798.t1 | exon | g5798.t1.exon1 | 11983605 | 11983646 |
| chr_2 | g5798 | g5798.t1 | cds | g5798.t1.CDS1 | 11983605 | 11983646 |
| chr_2 | g5798 | g5798.t1 | exon | g5798.t1.exon2 | 11983769 | 11984710 |
| chr_2 | g5798 | g5798.t1 | cds | g5798.t1.CDS2 | 11983769 | 11984710 |
| chr_2 | g5798 | g5798.t1 | TTS | g5798.t1 | 11984784 | 11984784 |
Sequences
>g5798.t1 Gene=g5798 Length=984
ATGGCTGATAGTAAAATAACTTATGTTCAATGCGATGGCTTGGCTGCTATGAAAATAGTA
AAACATTGTCATGAGGAATCACAAGGAAATATGGAAATCGCACAAGGAGCACTTCTCGGT
TTAGCGGAAGGAAATAGACTGGAAATTACAAATTGTTTTCCTTTCCCAAAATCAACAGAC
GAGAGTGTCGATGAAGAAGAATATCAACTTCAAATGATGAGAAGATTAAGACGAGTAAAT
GTAGATCACTTTCATGTTGGCTGGTATCAATCATCTGACATTGGCAATTTTTTGTCATTG
ACACTATTAGAGTCTCAATATCATTATCAAACAAGTATCGAAGAAGCAGTGGTTGTTGTT
TATGACACTCAAAAGTCAGCTGGAGGATTTCTTACATTAAAAGCTTATCGTTTAACACCG
CAAGCTATTCAAATGTACAAGGATGGTGATTTTACTCCTGATGCACTTCGTCAATTGAAA
ATTGGTTACGAAAAATTATTTGCTGAAATTCCAATTCACATCAAAAATTCCACTTTATCA
AACATCATGATGCTCGAATTAAAAGATATGGTACAAGAAGAAGAAGGCTCTCATTTTCTT
GACTTGGGAACAGCTGGTACTCTTGAGAATCACATTCGTGCAATGATGGATCGAGTTGAT
GAATTATATCAAGAAGCAAGTAAATTTAACAAGTATCAACAAACTGTTATGCGTCAAGAA
CAAGATAAGCATCGTCAACTGAATAGATTGGCACAAGAAAATGCAGCTCGAGTTGCTAAG
GGTGAACAACCATTACCCGAAGATGATGTCCTTAAACAATTCCGACCTCTACCCGTTCCA
CCAAGACTCAATCCAATGATTGTATCAGGACAAATTAACACCATTTCACAGCACATTAAT
CAATTCTGTTCGCAGTCGCTCGCTAAGCTTTATTTGACTCAGGCTCTTCAAGGTGCCAAA
GAAGCCAGAGGAGAATCAAAGTAA
>g5798.t1 Gene=g5798 Length=327
MADSKITYVQCDGLAAMKIVKHCHEESQGNMEIAQGALLGLAEGNRLEITNCFPFPKSTD
ESVDEEEYQLQMMRRLRRVNVDHFHVGWYQSSDIGNFLSLTLLESQYHYQTSIEEAVVVV
YDTQKSAGGFLTLKAYRLTPQAIQMYKDGDFTPDALRQLKIGYEKLFAEIPIHIKNSTLS
NIMMLELKDMVQEEEGSHFLDLGTAGTLENHIRAMMDRVDELYQEASKFNKYQQTVMRQE
QDKHRQLNRLAQENAARVAKGEQPLPEDDVLKQFRPLPVPPRLNPMIVSGQINTISQHIN
QFCSQSLAKLYLTQALQGAKEARGESK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5798.t1 | CDD | cd08065 | MPN_eIF3h | 7 | 269 | 1.25444E-126 |
| 6 | g5798.t1 | Coils | Coil | Coil | 319 | 327 | - |
| 5 | g5798.t1 | Gene3D | G3DSA:3.40.140.10 | Cytidine Deaminase | 2 | 194 | 7.8E-42 |
| 4 | g5798.t1 | Hamap | MF_03007 | Eukaryotic translation initiation factor 3 subunit H [EIF3H]. | 4 | 319 | 39.699837 |
| 2 | g5798.t1 | PANTHER | PTHR10410:SF3 | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H | 3 | 317 | 1.8E-105 |
| 3 | g5798.t1 | PANTHER | PTHR10410 | EUKARYOTIC TRANSLATION INITIATION FACTOR 3 -RELATED | 3 | 317 | 1.8E-105 |
| 1 | g5798.t1 | Pfam | PF01398 | JAB1/Mov34/MPN/PAD-1 ubiquitin protease | 7 | 114 | 1.6E-13 |
| 9 | g5798.t1 | ProSiteProfiles | PS50249 | MPN domain profile. | 9 | 142 | 21.139 |
| 8 | g5798.t1 | SMART | SM00232 | pad1_6 | 8 | 141 | 2.6E-19 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5798/g5798.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5798.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003743 | translation initiation factor activity | MF |
| GO:0008237 | metallopeptidase activity | MF |
| GO:0005515 | protein binding | MF |
| GO:0070122 | isopeptidase activity | MF |
| GO:0005852 | eukaryotic translation initiation factor 3 complex | CC |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K03247 (translation initiation factor 3 subunit H)
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.
