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.t3 TSS g5798.t3 11983529 11983529
chr_2 g5798 g5798.t3 isoform g5798.t3 11983605 11984710
chr_2 g5798 g5798.t3 exon g5798.t3.exon1 11983605 11983650
chr_2 g5798 g5798.t3 exon g5798.t3.exon2 11983769 11984710
chr_2 g5798 g5798.t3 cds g5798.t3.CDS1 11983775 11984710
chr_2 g5798 g5798.t3 TTS g5798.t3 11984784 11984784

Sequences

>g5798.t3 Gene=g5798 Length=988
ATGGCTGATAGTAAAATAACTTATGTTCAATGCGATGGCTTGGTAAGCTGCTATGAAAAT
AGTAAAACATTGTCATGAGGAATCACAAGGAAATATGGAAATCGCACAAGGAGCACTTCT
CGGTTTAGCGGAAGGAAATAGACTGGAAATTACAAATTGTTTTCCTTTCCCAAAATCAAC
AGACGAGAGTGTCGATGAAGAAGAATATCAACTTCAAATGATGAGAAGATTAAGACGAGT
AAATGTAGATCACTTTCATGTTGGCTGGTATCAATCATCTGACATTGGCAATTTTTTGTC
ATTGACACTATTAGAGTCTCAATATCATTATCAAACAAGTATCGAAGAAGCAGTGGTTGT
TGTTTATGACACTCAAAAGTCAGCTGGAGGATTTCTTACATTAAAAGCTTATCGTTTAAC
ACCGCAAGCTATTCAAATGTACAAGGATGGTGATTTTACTCCTGATGCACTTCGTCAATT
GAAAATTGGTTACGAAAAATTATTTGCTGAAATTCCAATTCACATCAAAAATTCCACTTT
ATCAAACATCATGATGCTCGAATTAAAAGATATGGTACAAGAAGAAGAAGGCTCTCATTT
TCTTGACTTGGGAACAGCTGGTACTCTTGAGAATCACATTCGTGCAATGATGGATCGAGT
TGATGAATTATATCAAGAAGCAAGTAAATTTAACAAGTATCAACAAACTGTTATGCGTCA
AGAACAAGATAAGCATCGTCAACTGAATAGATTGGCACAAGAAAATGCAGCTCGAGTTGC
TAAGGGTGAACAACCATTACCCGAAGATGATGTCCTTAAACAATTCCGACCTCTACCCGT
TCCACCAAGACTCAATCCAATGATTGTATCAGGACAAATTAACACCATTTCACAGCACAT
TAATCAATTCTGTTCGCAGTCGCTCGCTAAGCTTTATTTGACTCAGGCTCTTCAAGGTGC
CAAAGAAGCCAGAGGAGAATCAAAGTAA

>g5798.t3 Gene=g5798 Length=311
MKIVKHCHEESQGNMEIAQGALLGLAEGNRLEITNCFPFPKSTDESVDEEEYQLQMMRRL
RRVNVDHFHVGWYQSSDIGNFLSLTLLESQYHYQTSIEEAVVVVYDTQKSAGGFLTLKAY
RLTPQAIQMYKDGDFTPDALRQLKIGYEKLFAEIPIHIKNSTLSNIMMLELKDMVQEEEG
SHFLDLGTAGTLENHIRAMMDRVDELYQEASKFNKYQQTVMRQEQDKHRQLNRLAQENAA
RVAKGEQPLPEDDVLKQFRPLPVPPRLNPMIVSGQINTISQHINQFCSQSLAKLYLTQAL
QGAKEARGESK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g5798.t3 CDD cd08065 MPN_eIF3h 1 253 0.00000
6 g5798.t3 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase 1 178 0.00000
4 g5798.t3 Hamap MF_03007 Eukaryotic translation initiation factor 3 subunit H [EIF3H]. 1 303 37.68778
2 g5798.t3 PANTHER PTHR10410:SF3 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT H 1 301 0.00000
3 g5798.t3 PANTHER PTHR10410 EUKARYOTIC TRANSLATION INITIATION FACTOR 3 -RELATED 1 301 0.00000
1 g5798.t3 Pfam PF01398 JAB1/Mov34/MPN/PAD-1 ubiquitin protease 1 98 0.00000
7 g5798.t3 ProSiteProfiles PS50249 MPN domain profile. 1 126 19.76500
5 g5798.t3 SMART SM00232 pad1_6 1 125 0.00000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5798/g5798.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5798.t3.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