Gene loci information

Transcript annotation

  • This transcript has been annotated as Eukaryotic translation initiation factor 3 subunit H.

Parent gene

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.t4 TSS g5798.t4 11983529 11983529
chr_2 g5798 g5798.t4 isoform g5798.t4 11983809 11984764
chr_2 g5798 g5798.t4 exon g5798.t4.exon1 11983809 11984764
chr_2 g5798 g5798.t4 cds g5798.t4.CDS1 11983817 11984710
chr_2 g5798 g5798.t4 TTS g5798.t4 11984784 11984784

Sequences

>g5798.t4 Gene=g5798 Length=956
AAGGAAATATGGAAATCGCACAAGGAGCACTTCTCGGTTTAGCGGAAGGAAATAGACTGG
AAATTACAAATTGTTTTCCTTTCCCAAAATCAACAGACGAGAGTGTCGATGAAGAAGAAT
ATCAACTTCAAATGATGAGAAGATTAAGACGAGTAAATGTAGATCACTTTCATGTTGGCT
GGTATCAATCATCTGACATTGGCAATTTTTTGTCATTGACACTATTAGAGTCTCAATATC
ATTATCAAACAAGTATCGAAGAAGCAGTGGTTGTTGTTTATGACACTCAAAAGTCAGCTG
GAGGATTTCTTACATTAAAAGCTTATCGTTTAACACCGCAAGCTATTCAAATGTACAAGG
ATGGTGATTTTACTCCTGATGCACTTCGTCAATTGAAAATTGGTTACGAAAAATTATTTG
CTGAAATTCCAATTCACATCAAAAATTCCACTTTATCAAACATCATGATGCTCGAATTAA
AAGATATGGTACAAGAAGAAGAAGGCTCTCATTTTCTTGACTTGGGAACAGCTGGTACTC
TTGAGAATCACATTCGTGCAATGATGGATCGAGTTGATGAATTATATCAAGAAGCAAGTA
AATTTAACAAGTATCAACAAACTGTTATGCGTCAAGAACAAGATAAGCATCGTCAACTGA
ATAGATTGGCACAAGAAAATGCAGCTCGAGTTGCTAAGGGTGAACAACCATTACCCGAAG
ATGATGTCCTTAAACAATTCCGACCTCTACCCGTTCCACCAAGACTCAATCCAATGATTG
TATCAGGACAAATTAACACCATTTCACAGCACATTAATCAATTCTGTTCGCAGTCGCTCG
CTAAGCTTTATTTGACTCAGGCTCTTCAAGGTGCCAAAGAAGCCAGAGGAGAATCAAAGT
AATTTAATTTCCTCATTATGTGAACAATTTTTATGCATTAACAAAATAATCCAGAA

>g5798.t4 Gene=g5798 Length=297
MEIAQGALLGLAEGNRLEITNCFPFPKSTDESVDEEEYQLQMMRRLRRVNVDHFHVGWYQ
SSDIGNFLSLTLLESQYHYQTSIEEAVVVVYDTQKSAGGFLTLKAYRLTPQAIQMYKDGD
FTPDALRQLKIGYEKLFAEIPIHIKNSTLSNIMMLELKDMVQEEEGSHFLDLGTAGTLEN
HIRAMMDRVDELYQEASKFNKYQQTVMRQEQDKHRQLNRLAQENAARVAKGEQPLPEDDV
LKQFRPLPVPPRLNPMIVSGQINTISQHINQFCSQSLAKLYLTQALQGAKEARGESK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5798.t4 CDD cd08065 MPN_eIF3h 2 239 0.0000000
6 g5798.t4 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 2 164 0.0000000
4 g5798.t4 Hamap MF_03007 Eukaryotic translation initiation factor 3 subunit H [EIF3H]. 1 289 35.4611740
2 g5798.t4 PANTHER PTHR10410:SF3 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H 3 287 0.0000000
3 g5798.t4 PANTHER PTHR10410 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 -RELATED 3 287 0.0000000
1 g5798.t4 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 5 84 0.0000000
7 g5798.t4 ProSiteProfiles PS50249 MPN domain profile. 1 112 17.1800000
5 g5798.t4 SMART SM00232 pad1_6 1 111 0.0000003

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5798/g5798.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5798.t4.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

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.

Raw TPM values