General information for g1816.t1
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.t1 | isoform | g1816.t1 | 13161919 | 13166298 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon1 | 13161919 | 13162091 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS1 | 13161919 | 13162091 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon2 | 13162173 | 13162356 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS2 | 13162173 | 13162356 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon3 | 13162420 | 13162931 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS3 | 13162420 | 13162931 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon4 | 13163000 | 13163113 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS4 | 13163000 | 13163113 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon5 | 13163434 | 13163559 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS5 | 13163434 | 13163559 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon6 | 13163626 | 13165039 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS6 | 13163626 | 13165039 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon7 | 13165105 | 13165792 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS7 | 13165105 | 13165792 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon8 | 13165848 | 13166146 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS8 | 13165848 | 13166146 |
| chr_3 | g1816 | g1816.t1 | exon | g1816.t1.exon9 | 13166215 | 13166298 |
| chr_3 | g1816 | g1816.t1 | cds | g1816.t1.CDS9 | 13166215 | 13166298 |
| chr_3 | g1816 | g1816.t1 | TSS | g1816.t1 | 13166516 | 13166516 |
| chr_3 | g1816 | g1816.t1 | TTS | g1816.t1 | NA | NA |
Sequences
>g1816.t1 Gene=g1816 Length=3594
ATGGATCAAATGCCGTTCGATCAGCCATCGGCAATTCTTAGGGGACCTAGACCAATAGCA
CAAAATAGCATTAGTCCGCATCAGTGCTTTATTCCTGCGATGTTTCCTGTAATTGTAGGA
CCTCCATCAAATGTTCACCCATACGCGACATTTTATCGGCAACCTAGTGTGGTGCCACCT
CCAATATTACCGGTAGTACATTATACAAAGCAGCCAACGCAAGTAGAACATCCAACTAAA
AAAAGTCATGCTTTACAAATTCGTGATCCAGTAACAGGCAAAGATATCATTGAAAGCTTT
AAACATGAAAAAACTGGATCGTTAAACAAAGATGCTAAAGAATTTAGGCCATGTAATATT
CATCAAAAGACAGCTATACAAAGTGAAAAAGACGGTACTAGAATAAAAACTTCTTCACCG
ATACAAAAGAATGATGATATGTCAATTATACAAGAAGATATATCAATTGTACAAGAAGAA
GATGTTTCCAGTCCAATTAAGTGTACAATTGGCAATGAAAATTTTACTGGTGACGATTTT
AGTAGAAACTACAGATACACAAAGGAAGAATTATTAATGCTAAAAGAAAGTCTTGCAGTT
GAGAAATCTAAACCGCCTCAGTTTTCACATAGTTCATTGATTTGCGATGATTTGGATTTG
ACTATATATAGAATACTTTTTGATAAAACCTATCAAGATTCTACCTTTAATGATTCATAT
GATATCTCAAACTCATCATATAACAAGACCAATTCTTCTTTGTCTTTAAGGCGTAGTTTT
CAAGATAGTCATTCTAGTTCTCGCAACAACAGAACACCAGAAAAGAAAAGTATCATTAGA
ATGACAATGAGTCAACCAAACATACGATTAAATGAAGCAGAAAACGCATGGGTGCCATCG
CATTTGAAACTAAAGATTCGAAAGAGTGATGAAGAAGAAAAGCTTGAAAAACTCAAGAAA
AACTTTCGTTCATTATTAAACAAAATCACTGCTGAAAATTTTGAACATATCGCTAAAGAA
GCTTCTAATACAAACAAATTTTCAATAACTGAGAAAGAAAGTTTAGAATCGATTGTTGAT
ATTCTTTTTGAGAAATCAATTACAGAACCTGGATTTGCTCCAATCTATGCTCGGTTATGT
AAGGTTCTTACAGAGGCTCATGTTTTTCAAACGACAGATATAAATGGAAACGAATCGAAG
AAAAGTCCTTGGAAAATGTATTTAATTTACAGATGTCAAGAAGAATTTGAAAGATTTTCA
GTTGATGAAGAGACATTAAATGAAATTTTGAGTAAGATCGACTCTGCAGAAACTCAAGAA
GATAAGGATTATTATGCTGATATCCATTTCAATTATCGTTATCGTGCTCAAGGAACAATT
AAATTTATTGGAGAGTTGTATATGTATGATTTGCTTAATTCAAATGTCATGAAAAGTTGT
ATTGAGTCTCTTCTTTCATCAATAACTGAAGAAAACATCTCTCGAGTTTGTCATCTCTTT
ACGACAATTGGTAAAAAATTTGAAGAAAATCCACCAAAGGATCAAAACGGAACGGAACTT
ATTGATAAGTACATGGAACAACTGCAGCGTTTAAAGAACAATAAATGTATTACGACATCT
CGCATTAAATTTGATATAATGAATGTTATAGATCTGCGAAAAGCAAATTGGAAGCCACGA
GAAAATGCTAAATTAGTGGTTAAGCCCAAGACATTCAATGAATTAAAAGAAGAAATTAAA
AAGGAAAAGGAGAAACAAGAAAAAACTCTGAGCACATATCAACCATCAAAAAATGTTACA
ATGCAGTCACACAATAATTTTCAAAATCAGAACCAAAGATTCAAATCACATCAACAACCA
CGAACTTTCTCAAATATGGTTAACATTGATTTCAATAAAATTGGTTTGAATTCGAAAGAA
GTTACCTTGGCACCTCAAACCAAAAGTTTAACGTTTAGAAGCTTAGAACCAAAATCATTG
CTAATAAGCAATGCATTTGGAGCTCTAAAAGTAGATTGTGATGATCAAGAATTGCCGTCA
ACAATGCACTCATCACGTGCAAATACAAATAAAAACAGTAGAAAGGAAAAAGTACATCAA
CAACAAATCACAACTCAAAATTCTGTTGATGAAAACTCTGATGACATTTTTACTATCGAC
CTTAGCAACTCTGAGCAATTAATTTTTGAAAATTGTTTAAAAAAGTTCGAAGCATTTATT
AAAGGAAAACTTACTATGGAAATGATGATTACTGACATGAGAGACATCAAAATAACTGAT
CGAATTCTTGCAATGATTTATAATGCTTACCTTGATAAAAAGGAACTTGATCAGTATGGA
TTTATTAAAGCGCTTATAAATTTATTAAAAGCAAATTTAATCGACAAACAAGTAAATATT
GAAGCTATAGGATTACTTTTCAAGCTCATTCCTTTTTTGATTCCTGATGTGCCTCTAATC
AACACATATATAGGAGAATTTCTTGTAAAACTCCATAATGATCAAATGATATGTATCCAA
GACATTGATAAAATTTGTAACAACAAAGAAGCAAAGGGAGCTTTAAAATATTTACAAGAC
AGTATTGATGTTGATGTTTCTACCGAATCAACAAATTTAATCGACAAACAAGTAAATATT
GAAGCTATAGGATTACTTTTCAAGCTCATTCCTTTTTTGATTCCTGATGTGCCTCTAATC
AACACATATATAGGAGAATTTCTTGTAAAACTCCATAATGATCAAATGATATGTATCCAA
GACATTGATAAAATTTGTAACAACAAAGAAGCAAAGGGAGCTTTAAAATATTTACAAGAC
AGTATTGATGTTGATGCTTTTGATTTGAAAAATAAATCCGAGTTGAAAAACATGAAATCA
AACGAAAAGAAGTCAAATGTCTCTGATGTACAAATTGAAAAATCAACCAGTAAATCAAAA
AAACGAGATAACAAAGCTAAGAAAAATAAAAACAAACAAAATAACAAGAAGAAATCAAAA
CAGACAGAAAGACCTATCGAGCCTCCTGAAATTTTGTGTGAATCGTATAATTGTAATAAT
GTCGAAATTTCACCCATATCGACAGACAATATGAATGTTCAAAACGAGTCAAATGTATCA
CATGAAGAAAATTCAGATGGATCTCAAACACAAAACATCAAGGCAGATCTCATGAAGAAG
ATAGCATTTCTACTAAAAAAGCAAAAGCCATTGGATGAAATTTATAAGCTTATAGATACA
TCAAATCAATCAAAAAAAATGAGCTTCATCTCAGAATTATCAAAAACTATCGGAAAAAAT
CTTAAATTTGATTCTTCAAAAAAGTATACTGATTACTACATGTTACTTGAACGTTATATA
GATAATGATATTAAAAAAGGAGCCGAATGTTTAAATGCAATTGCTGATACATTTGTTTCG
GAAAAAGCAGCACAGATCTTCGAGTTATATTATGAAAACAACGTTGTTCCTTGCGAATCG
TTAAAACTTTGGTGTCAAAATAAAGCAAAGAATGAGAAAAATAGCCAAGTAATGTACCAA
CTGCAAAATTTTCTCGCAACTCTAAACAACACTGAAGAGTTGAATTTAGAATAA
>g1816.t1 Gene=g1816 Length=1197
MDQMPFDQPSAILRGPRPIAQNSISPHQCFIPAMFPVIVGPPSNVHPYATFYRQPSVVPP
PILPVVHYTKQPTQVEHPTKKSHALQIRDPVTGKDIIESFKHEKTGSLNKDAKEFRPCNI
HQKTAIQSEKDGTRIKTSSPIQKNDDMSIIQEDISIVQEEDVSSPIKCTIGNENFTGDDF
SRNYRYTKEELLMLKESLAVEKSKPPQFSHSSLICDDLDLTIYRILFDKTYQDSTFNDSY
DISNSSYNKTNSSLSLRRSFQDSHSSSRNNRTPEKKSIIRMTMSQPNIRLNEAENAWVPS
HLKLKIRKSDEEEKLEKLKKNFRSLLNKITAENFEHIAKEASNTNKFSITEKESLESIVD
ILFEKSITEPGFAPIYARLCKVLTEAHVFQTTDINGNESKKSPWKMYLIYRCQEEFERFS
VDEETLNEILSKIDSAETQEDKDYYADIHFNYRYRAQGTIKFIGELYMYDLLNSNVMKSC
IESLLSSITEENISRVCHLFTTIGKKFEENPPKDQNGTELIDKYMEQLQRLKNNKCITTS
RIKFDIMNVIDLRKANWKPRENAKLVVKPKTFNELKEEIKKEKEKQEKTLSTYQPSKNVT
MQSHNNFQNQNQRFKSHQQPRTFSNMVNIDFNKIGLNSKEVTLAPQTKSLTFRSLEPKSL
LISNAFGALKVDCDDQELPSTMHSSRANTNKNSRKEKVHQQQITTQNSVDENSDDIFTID
LSNSEQLIFENCLKKFEAFIKGKLTMEMMITDMRDIKITDRILAMIYNAYLDKKELDQYG
FIKALINLLKANLIDKQVNIEAIGLLFKLIPFLIPDVPLINTYIGEFLVKLHNDQMICIQ
DIDKICNNKEAKGALKYLQDSIDVDVSTESTNLIDKQVNIEAIGLLFKLIPFLIPDVPLI
NTYIGEFLVKLHNDQMICIQDIDKICNNKEAKGALKYLQDSIDVDAFDLKNKSELKNMKS
NEKKSNVSDVQIEKSTSKSKKRDNKAKKNKNKQNNKKKSKQTERPIEPPEILCESYNCNN
VEISPISTDNMNVQNESNVSHEENSDGSQTQNIKADLMKKIAFLLKKQKPLDEIYKLIDT
SNQSKKMSFISELSKTIGKNLKFDSSKKYTDYYMLLERYIDNDIKKGAECLNAIADTFVS
EKAAQIFELYYENNVVPCESLKLWCQNKAKNEKNSQVMYQLQNFLATLNNTEELNLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g1816.t1 | Coils | Coil | Coil | 301 | 332 | - |
| 13 | g1816.t1 | Coils | Coil | Coil | 572 | 592 | - |
| 12 | g1816.t1 | Gene3D | G3DSA:1.25.40.180 | - | 320 | 572 | 2.0E-58 |
| 11 | g1816.t1 | Gene3D | G3DSA:1.25.40.180 | - | 746 | 865 | 2.9E-5 |
| 7 | g1816.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 277 | - |
| 8 | g1816.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 267 | - |
| 5 | g1816.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 681 | 706 | - |
| 9 | g1816.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 957 | 1008 | - |
| 10 | g1816.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 957 | 980 | - |
| 6 | g1816.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 981 | 995 | - |
| 2 | g1816.t1 | PANTHER | PTHR23253 | EUKARYOTIC TRANSLATION INITIATION FACTOR 4 GAMMA | 111 | 837 | 1.0E-64 |
| 1 | g1816.t1 | Pfam | PF02854 | MIF4G domain | 322 | 555 | 1.3E-31 |
| 4 | g1816.t1 | SMART | SM00543 | if4_15 | 319 | 556 | 4.1E-31 |
| 3 | g1816.t1 | SUPERFAMILY | SSF48371 | ARM repeat | 311 | 559 | 1.53E-46 |
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.
