General information for g1159.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative RNA-binding protein squid.
Parent gene
- The parent gene g1159 is located on chr_3: 8431212..8432548 (+ 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 | g1159 | g1159.t20 | isoform | g1159.t20 | 8426535 | 8431942 |
| chr_3 | g1159 | g1159.t20 | exon | g1159.t20.exon1 | 8426535 | 8426809 |
| chr_3 | g1159 | g1159.t20 | exon | g1159.t20.exon2 | 8426874 | 8427099 |
| chr_3 | g1159 | g1159.t20 | cds | g1159.t20.CDS1 | 8426883 | 8427099 |
| chr_3 | g1159 | g1159.t20 | exon | g1159.t20.exon3 | 8427224 | 8427421 |
| chr_3 | g1159 | g1159.t20 | cds | g1159.t20.CDS2 | 8427224 | 8427421 |
| chr_3 | g1159 | g1159.t20 | exon | g1159.t20.exon4 | 8430907 | 8431131 |
| chr_3 | g1159 | g1159.t20 | cds | g1159.t20.CDS3 | 8430907 | 8430971 |
| chr_3 | g1159 | g1159.t20 | exon | g1159.t20.exon5 | 8431212 | 8431942 |
| chr_3 | g1159 | g1159.t20 | TTS | g1159.t20 | 8431937 | 8431937 |
| chr_3 | g1159 | g1159.t20 | TSS | g1159.t20 | NA | NA |
Sequences
>g1159.t20 Gene=g1159 Length=1655
AGGAATTGCGTGATCATTTTGGACAATATGGTGAAATTGACAGCATCAATGTTAAAACAG
ATCCTACAACTGGTCGCTCACGTGGATTTGCATTCATTGTTTATAAAGCAGCTGATTCAA
TTGATAAAGTTGTCGCTGCTGGTGATCATATCATTAACAACAAGAAAGTTGATCCTAAAA
AAGCCAAGGCAAGAACTGGCAAAATCTTTGTCGGTGGACTCATTCCAGAAATTAGTGATG
ATGAAATCAAGGCATATTTCTCACAATTTGGAAATATTACTGAAATGGAAATGCCATTCG
ATAAGCAAAAGAATCAACGTAAAGCTTTCTGCTTTATCACTTTTGACTCGGAAGCTGTTG
TCAATGAATTATTAAAGTCTCCAAAACAAACAATCAGTGGAAAGGAAGTTGATGTCAAAA
AAGCCACGCCAAAACCAGATAATGCTCCAATGATGCAACGTGGTGGAGGACGAAATATGA
GAGGTGGACGAGGAGGACGCGGATTTCAAGGAAATTGGAACGGATATGGAGGTGGTTATG
GCCAAAACGGCTGGAACCAAGGCGGAGGCAGTTGGGGTGGAAACAACTATGACAATTATC
AGGGTGGTTATGGTGGTAGTGGTGTTGATTATCAGGGTAACTATGGCGGATACAACAATT
ATGATTATGGAAATTACGGCGGCAGCGGTGGCAATTATGGCGGAAACTACCAAGGTGGAA
AACAAAGAGGTGGTGGGCGTCAACAAAGACATCAACCATATTAAGCCATTTTTCTTGGAT
TAAGTAAAAATACAAACAACTCATCCATCTCATTCACTCATTGAAATCCTTAATTGTATT
TTTTGAACATAAATTATAATATCGACCGTGTCTTCAAAATGAAAAAGAATATTAAACAAT
AGCAGCAAAAACCAATCAAGAAAAACTCTCATCAAATGTTGAATTTATATATGCGTATAT
AAAATTCTCACATACCATCATCAACAATAAATAAGATTTACAAGAACAACTCATTTTAAT
ATACATTGTTGTATGGGCGATTCATTCCACATTAAATACACACACAAACAAACCATTTTT
TACATTACTAAATAAATCAGAAGGAAATGTAAATTTTTAATATTCTCTCTATCTCTCATT
GTTCTGTATATTTTGACTGAATTTTTTTTTCTTTTTAATTTCTATTTGTGAGATACTTAT
GAGAAAGGATAGTATGTAATTAAAACAATCAACATTTGAAATATCTTTAGCATTCAAAGA
CGACCTCGATATATAAGATCTTTAACATCAAAAAACAACCCTCCTCATACATAATTTTTT
TATCCCTCTGATTTTCTTCATTAATGTCTTGCATTCATAAATTAATAGCTTTTTGATTTT
AAAAAATTTTTCTTACTCAATAATTGAGTTGACTAAAAACACAAACAAATAGTACGGTTT
TCGATTATTGAAGAAGGAAAATGAGTATATAAAATTTATAATTCTCTCATCAATTAAATT
TATTACACAAAAATAGTAATTTAAATGATAAAAAGAATAATTACAGTAGCGTTAATTCAC
TTGATAACTTTATAAAGAAAATAACTATTTTTAATCATCATTTCTAAGGATAAAAATTAA
TAAAACCTCTTATAAGATTAAATTTAAAACAAAAA
>g1159.t20 Gene=g1159 Length=159
MEMPFDKQKNQRKAFCFITFDSEAVVNELLKSPKQTISGKEVDVKKATPKPDNAPMMQRG
GGRNMRGGRGGRGFQGNWNGYGGGYGQNGWNQGGGSWGGNNYDNYQGGYGGSGVDYQGNY
GGYNNYDYGNYGGSGGNYGGNYQGGKQRGGGRQQRHQPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g1159.t20 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 81 | 1.4E-8 |
| 5 | g1159.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 41 | 68 | - |
| 4 | g1159.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 139 | 159 | - |
| 1 | g1159.t20 | PANTHER | PTHR48033:SF8 | RNA-BINDING PROTEIN SQUID | 1 | 159 | 2.7E-36 |
| 2 | g1159.t20 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 1 | 159 | 2.7E-36 |
| 3 | g1159.t20 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 2 | 77 | 6.28E-11 |
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:0003676 | nucleic acid 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.
