General information for g1816.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Eukaryotic translation initiation factor 4 gamma 1.
Parent gene
- The parent gene g1816 is located on chr_3: 13165034..13166430 (- 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_3 | g1816 | g1816.t2 | isoform | g1816.t2 | 13164370 | 13166430 |
| chr_3 | g1816 | g1816.t2 | exon | g1816.t2.exon1 | 13164370 | 13165039 |
| chr_3 | g1816 | g1816.t2 | cds | g1816.t2.CDS1 | 13164371 | 13165039 |
| chr_3 | g1816 | g1816.t2 | exon | g1816.t2.exon2 | 13165105 | 13165774 |
| chr_3 | g1816 | g1816.t2 | cds | g1816.t2.CDS2 | 13165105 | 13165737 |
| chr_3 | g1816 | g1816.t2 | exon | g1816.t2.exon3 | 13165831 | 13166146 |
| chr_3 | g1816 | g1816.t2 | exon | g1816.t2.exon4 | 13166215 | 13166304 |
| chr_3 | g1816 | g1816.t2 | exon | g1816.t2.exon5 | 13166410 | 13166430 |
| chr_3 | g1816 | g1816.t2 | TSS | g1816.t2 | 13166516 | 13166516 |
| chr_3 | g1816 | g1816.t2 | TTS | g1816.t2 | NA | NA |
Sequences
>g1816.t2 Gene=g1816 Length=1767
TCTATAACGAAAAACAATCTAGTGAAAATGGATCAAATGCCGTTCGATCAGCCATCGGCA
ATTCTTAGGGGACCTAGACCAATAGCACAAAATAGCATTAGTCCGCATCAGTGCTTTATT
CCTGCGATGTTTCCTGTAATTGTAGGACCTCCATCAAATGTTCACCCATACGCGACATTT
TATCGGCAACCTAGTGTGGTGCCACCTCCAATATTACCGGTAGTACATTATACAAAGCAG
CCAACGCAAGTAGAACATCCAACTAAAAAAAGTCATGCTTTACAAATTCGTGATCCAGTA
ACAGGCAAAGATATCATTGAAAGCTTTAAACATGAAAAAACTGGATCGTTAAACAAAGAT
GCTAAAGAATTTAGGCCATGTAATATTCATCAAAAGACAGCTATACAAAGGTAAAAACAC
AATTCATAATAAAAACTTCTTCACCGATACAAAAGAATGATGATATGTCAATTATACAAG
AAGATATATCAATTGTACAAGAAGAAGATGTTTCCAGTCCAATTAAGTGTACAATTGGCA
ATGAAAATTTTACTGGTGACGATTTTAGTAGAAACTACAGATACACAAAGGAAGAATTAT
TAATGCTAAAAGAAAGTCTTGCAGTTGAGAAATCTAAACCGCCTCAGTTTTCACATAGTT
CATTGATTTGCGATGATTTGGATTTGACTATATATAGAATACTTTTTGATAAAACCTATC
AAGATTCTACCTTTAATGATTCATATGATATCTCAAACTCATCATATAACAAGACCAATT
CTTCTTTGTCTTTAAGGCGTAGTTTTCAAGATAGTCATTCTAGTTCTCGCAACAACAGAA
CACCAGAAAAGAAAAGTATCATTAGAATGACAATGAGTCAACCAAACATACGATTAAATG
AAGCAGAAAACGCATGGGTGCCATCGCATTTGAAACTAAAGATTCGAAAGAGTGATGAAG
AAGAAAAGCTTGAAAAACTCAAGAAAAACTTTCGTTCATTATTAAACAAAATCACTGCTG
AAAATTTTGAACATATCGCTAAAGAAGCTTCTAATACAAACAAATTTTCAATAACTGAGA
AAGAAAGTTTAGAATCGATTGTTGATATTCTTTTTGAGAAATCAATTACAGAACCTGGAT
TTGCTCCAATCTATGCTCGGTTATGTAAGGTTCTTACAGAGGCTCATGTTTTTCAAACGA
CAGATATAAATGGAAACGAATCGAAGAAAAGTCCTTGGAAAATGTATTTAATTTACAGAT
GTCAAGAAGAATTTGAAAGATTTTCAGTTGATGAAGAGACATTAAATGAAATTTTGAGTA
AGATCGACTCTGCAGAAACTCAAGAAGATAAGGATTATTATGCTGATATCCATTTCAATT
ATCGTTATCGTGCTCAAGGAACAATTAAATTTATTGGAGAGTTGTATATGTATGATTTGC
TTAATTCAAATGTCATGAAAAGTTGTATTGAGTCTCTTCTTTCATCAATAACTGAAGAAA
ACATCTCTCGAGTTTGTCATCTCTTTACGACAATTGGTAAAAAATTTGAAGAAAATCCAC
CAAAGGATCAAAACGGAACGGAACTTATTGATAAGTACATGGAACAACTGCAGCGTTTAA
AGAACAATAAATGTATTACGACATCTCGCATTAAATTTGATATAATGAATGTTATAGATC
TGCGAAAAGCAAATTGGAAGCCACGAGAAAATGCTAAATTAGTGGTTAAGCCCAAGACAT
TCAATGAATTAAAAGAAGAAATTAAAA
>g1816.t2 Gene=g1816 Length=434
MSIIQEDISIVQEEDVSSPIKCTIGNENFTGDDFSRNYRYTKEELLMLKESLAVEKSKPP
QFSHSSLICDDLDLTIYRILFDKTYQDSTFNDSYDISNSSYNKTNSSLSLRRSFQDSHSS
SRNNRTPEKKSIIRMTMSQPNIRLNEAENAWVPSHLKLKIRKSDEEEKLEKLKKNFRSLL
NKITAENFEHIAKEASNTNKFSITEKESLESIVDILFEKSITEPGFAPIYARLCKVLTEA
HVFQTTDINGNESKKSPWKMYLIYRCQEEFERFSVDEETLNEILSKIDSAETQEDKDYYA
DIHFNYRYRAQGTIKFIGELYMYDLLNSNVMKSCIESLLSSITEENISRVCHLFTTIGKK
FEENPPKDQNGTELIDKYMEQLQRLKNNKCITTSRIKFDIMNVIDLRKANWKPRENAKLV
VKPKTFNELKEEIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1816.t2 | Coils | Coil | Coil | 155 | 186 | - |
| 7 | g1816.t2 | Gene3D | G3DSA:1.25.40.180 | - | 173 | 426 | 3.1E-59 |
| 5 | g1816.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 107 | 121 | - |
| 6 | g1816.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 107 | 131 | - |
| 2 | g1816.t2 | PANTHER | PTHR23253 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA | 31 | 432 | 1.4E-60 |
| 1 | g1816.t2 | Pfam | PF02854 | MIF4G domain | 176 | 409 | 1.6E-32 |
| 4 | g1816.t2 | SMART | SM00543 | if4_15 | 173 | 410 | 4.1E-31 |
| 3 | g1816.t2 | SUPERFAMILY | SSF48371 | ARM repeat | 165 | 413 | 1.78E-47 |
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:0003723 | RNA binding | MF |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed