General information for g5961.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GATOR complex protein MIOS.
Parent gene
- The parent gene g5961 is located on chr_2: 13024410..13027053 (+ 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 | g5961 | g5961.t1 | TSS | g5961.t1 | 13024364 | 13024364 |
| chr_2 | g5961 | g5961.t1 | isoform | g5961.t1 | 13024410 | 13027053 |
| chr_2 | g5961 | g5961.t1 | exon | g5961.t1.exon1 | 13024410 | 13024545 |
| chr_2 | g5961 | g5961.t1 | cds | g5961.t1.CDS1 | 13024410 | 13024545 |
| chr_2 | g5961 | g5961.t1 | exon | g5961.t1.exon2 | 13024616 | 13027053 |
| chr_2 | g5961 | g5961.t1 | cds | g5961.t1.CDS2 | 13024616 | 13027053 |
| chr_2 | g5961 | g5961.t1 | TTS | g5961.t1 | 13027133 | 13027133 |
Sequences
>g5961.t1 Gene=g5961 Length=2574
ATGATAAGCTATTTTAAAAATTCTAAAGACAAATTCGCACTTGCGACAGGATCTGAAGTA
AGTCTTTTTCAATTAAAAGAACGCGATAATGTTGAAGATTTTAGAATTTATGATGATCCA
AAGCCACAAACAATAAACCAAATAAAATTCATCAGTCAACATAATTCAACCCTCACTTAC
CTCAACTCAGAAAAACGCTACCAGTACATTAAGTGCATTGCAACATCATTTCATGAAAAT
GAATTGTTAGTAGCAACTGGTCAAGTCTCGGGAAAAGTGATGATTGTAGATTTTGAGCCA
AAAAATGAGATCAATCTTGAATTTACTCCTCGTCAAAATCGACCATCACTTTCACTTGCA
TGGAATGAGCAAGAACAGAATTTATTGGCAATGGGATTTGATAAGAATAAATTCGATCAT
TCAATATCAGTCTGGGACATTTCTCGAGGCCAACCTAGTGAAAGTTCAATTGTAAATCTG
ATTGGTCTCAGTGAATCAGCGCATTCACTTTGTTGGGACTCACGAAAAAATCTCATAGCA
GGTATGAGTTCAAAGTATATTAAATTTATGGATCTGCGAGCAAATCAAGTTCAAACCGTC
AACACTCGAGCAGTTTGCGGATTAACAATATCATCAAATAATCGTTTATTAGCAAGTTAT
TACGATAATGTTGTAAACATTTTTGACCTTCGGAAGTTCACTGAACCTCTAAATCAATTT
CAATTGGCTAACAATCTCGCTCAAATATCGTGGTGTTCATCGTCTCAAAATTGCCTCTTG
TGCCTTCAAAAAGATAACTCGTTAACTATCAATATAATTGATATACATGGAAATGGAACA
GAAGAGGACAATGATAGCACACATTTTGTTAAACGAGTTATTGCTCCATTTGAAATTGTT
GATCGAAAAAATAAACATCAATTACAAACTAAAGCAACTGCACTTGAAAACATTTGCTGG
CATCCAAAAATTTCATCAAATCGAATGATTTGCAGTGCATCAAATTCAAATAATTCAATT
TTGCTTATGGAATTCGATGTGCCGCAACGTAGAATTGCAGTTTTTGATAAATGGAATAAA
GTTTATGCACCGACTCATAACGAAATTCGTGACATTCCAGTCTCATCACCACCATCGTCA
CCAACAAATTCAACAAATTCATGGTATCCAAATGCTAATTACATTGATGGTGATATTTCA
GAACTTTTTCAACAAAGAATTCTACAAGATTATGGACAAATGGACTTTGAAAGAAATGCA
AAAGTTAGCATGGATTCAACTTTAGCAAGCGTTTGGAAAATGCTCGGGCAAATGTCAGCA
CAAGATTGCTTTATTGGCTTGCGGACTATCTTGGGAATTGACTCAAAAAGTAATGAACTT
ACGATAGCACAATCTGCGGTTGAAACGAGATCTTTTCAGGATTTTCCTTCGGGCGCTACA
ATTCGTATTTACAAAAGCGAGGAAAGAGAATTTGCAAAAGAGCTTTGTGGTTGGATGAAT
TTCGATAAGAATGATATGAGTGGAAACTTACAGATGTATATTGAGGAACTTTGTAAAAAG
AAACGTTTCACGCGGGCTGCCATGCTTGCAGTCTTTCATTTAAAAATTCGATTAGCATGT
GATATTTTGGGACGCGGTGCAAATGAAATGGAAGAGGAAAAAAGTTCACTAAGAATGTCA
GCAATCGCTTTAGCTGGTTATAATACTGGAAGCGTATGGAAGCTTCAATGCAGTTCAGCA
CAGATCGAAGATGCATACTTACGTGCTATTTTTTCATTTCTCTCTGATGACACTTATGCA
GGTGTGCTATACGAGGATGGTGTTTCAATTAGTGATCGAATGGCTTTTGCTTGCACGTTC
CTAAGCGACCGTCAACTATCAGAGTACGTGAAGCACATGATTCAGAATTGTATTGAGCGT
GGAGATTTAAGTGGATTACTTGTTACTGGCGCCACAATTGATGGCATTCAATTGCTGCAG
GCATTTGTTGATAGAACAGACGATGTACAGACAGCAGCATTGATTGGACAAAAGATATTA
CCAGCTGATTTGCAAACAGACAATCGACTACAAAGTTGGATTGCAATTTTACGGAACCTT
ATGAACACTTGGGAGATGTTTGAAAAACGTGCTGCATTTGATATCTCGATAGCTTCAGCA
AGAACTTCTCAAAAAATACCGAAATCAGTCTTTTTACTTTGTTCATTTTGTGGAAAATCA
GTTTCAGCGGCAGCTATTCAAGAAGATGCACGTGTAAGGAATCAAATGCAAACAAGTAAA
CTATCAAGTTGCCCAAACTGCCGAAAGCCTTTACCACGCTGTTCTCTCTGTTTGCTACAT
ATGGGAACATCATTGCCATCAAATTTCTATAATCCAACTAATATCAAATCACGCAACATC
AAATCTTGGTTTACTTGGTGTCAGAGTTGTCGTCATGGTGGTCATCTAGTTCACATTTCT
GAATGGTTTAAGAAAAATACCGAATGTCCAGTCACAAATTGCAATTGTAATTGTTTTCTA
ATCGATTTATCGCTATTAAAAGAAAAGAAAGAGAATGATACAGACGGCCATTAA
>g5961.t1 Gene=g5961 Length=857
MISYFKNSKDKFALATGSEVSLFQLKERDNVEDFRIYDDPKPQTINQIKFISQHNSTLTY
LNSEKRYQYIKCIATSFHENELLVATGQVSGKVMIVDFEPKNEINLEFTPRQNRPSLSLA
WNEQEQNLLAMGFDKNKFDHSISVWDISRGQPSESSIVNLIGLSESAHSLCWDSRKNLIA
GMSSKYIKFMDLRANQVQTVNTRAVCGLTISSNNRLLASYYDNVVNIFDLRKFTEPLNQF
QLANNLAQISWCSSSQNCLLCLQKDNSLTINIIDIHGNGTEEDNDSTHFVKRVIAPFEIV
DRKNKHQLQTKATALENICWHPKISSNRMICSASNSNNSILLMEFDVPQRRIAVFDKWNK
VYAPTHNEIRDIPVSSPPSSPTNSTNSWYPNANYIDGDISELFQQRILQDYGQMDFERNA
KVSMDSTLASVWKMLGQMSAQDCFIGLRTILGIDSKSNELTIAQSAVETRSFQDFPSGAT
IRIYKSEEREFAKELCGWMNFDKNDMSGNLQMYIEELCKKKRFTRAAMLAVFHLKIRLAC
DILGRGANEMEEEKSSLRMSAIALAGYNTGSVWKLQCSSAQIEDAYLRAIFSFLSDDTYA
GVLYEDGVSISDRMAFACTFLSDRQLSEYVKHMIQNCIERGDLSGLLVTGATIDGIQLLQ
AFVDRTDDVQTAALIGQKILPADLQTDNRLQSWIAILRNLMNTWEMFEKRAAFDISIASA
RTSQKIPKSVFLLCSFCGKSVSAAAIQEDARVRNQMQTSKLSSCPNCRKPLPRCSLCLLH
MGTSLPSNFYNPTNIKSRNIKSWFTWCQSCRHGGHLVHISEWFKKNTECPVTNCNCNCFL
IDLSLLKEKKENDTDGH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5961.t1 | CDD | cd16691 | mRING-H2-C3H3C2_Mio | 771 | 838 | 0 |
| 7 | g5961.t1 | Gene3D | G3DSA:2.130.10.10 | - | 9 | 344 | 0 |
| 2 | g5961.t1 | PANTHER | PTHR16453:SF9 | GATOR COMPLEX PROTEIN MIOS | 3 | 287 | 0 |
| 4 | g5961.t1 | PANTHER | PTHR16453 | WD40 DOMAIN-CONTAINING PROTEIN MIO FAMILY MEMBER | 3 | 287 | 0 |
| 3 | g5961.t1 | PANTHER | PTHR16453:SF9 | GATOR COMPLEX PROTEIN MIOS | 452 | 840 | 0 |
| 5 | g5961.t1 | PANTHER | PTHR16453 | WD40 DOMAIN-CONTAINING PROTEIN MIO FAMILY MEMBER | 452 | 840 | 0 |
| 1 | g5961.t1 | Pfam | PF17034 | Zinc-ribbon like family | 734 | 838 | 0 |
| 6 | g5961.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 67 | 350 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5961/g5961.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5961.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K20407 (SEA/GATOR complex protein SEA4/MIOS)
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.
