General information for g1159.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t12 | TSS | g1159.t12 | 8422719 | 8422719 |
| chr_3 | g1159 | g1159.t12 | isoform | g1159.t12 | 8422830 | 8431281 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon1 | 8422830 | 8422957 |
| chr_3 | g1159 | g1159.t12 | cds | g1159.t12.CDS1 | 8422830 | 8422957 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon2 | 8426427 | 8426467 |
| chr_3 | g1159 | g1159.t12 | cds | g1159.t12.CDS2 | 8426427 | 8426467 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon3 | 8426535 | 8426809 |
| chr_3 | g1159 | g1159.t12 | cds | g1159.t12.CDS3 | 8426535 | 8426809 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon4 | 8426874 | 8427099 |
| chr_3 | g1159 | g1159.t12 | cds | g1159.t12.CDS4 | 8426874 | 8427099 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon5 | 8427224 | 8427421 |
| chr_3 | g1159 | g1159.t12 | cds | g1159.t12.CDS5 | 8427224 | 8427421 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon6 | 8430907 | 8431131 |
| chr_3 | g1159 | g1159.t12 | cds | g1159.t12.CDS6 | 8430907 | 8430971 |
| chr_3 | g1159 | g1159.t12 | exon | g1159.t12.exon7 | 8431212 | 8431281 |
| chr_3 | g1159 | g1159.t12 | TTS | g1159.t12 | 8431937 | 8431937 |
Sequences
>g1159.t12 Gene=g1159 Length=1163
ATGGCTGATGTACAAGAATACGATAACGGCGAACAAATGCAAGAAGATTTCCAGGGACAA
GGTGATCAATCTGGAGATAGTAACTATCAAAACGGAAATGGAGAAACTCAAGCTCGCGAT
GACGATCGAAAGCTGTTTGTCGGTGGTTTAAGTTGGGAAACAACAGAAAAGGAATTGCGT
GATCATTTTGGACAATATGGTGAAATTGACAGCATCAATGTTAAAACAGATCCTACAACT
GGTCGCTCACGTGGATTTGCATTCATTGTTTATAAAGCAGCTGATTCAATTGATAAAGTT
GTCGCTGCTGGTGATCATATCATTAACAACAAGAAAGTTGATCCTAAAAAAGCCAAGGCA
AGAACTGGCAAAATCTTTGTCGGTGGACTCATTCCAGAAATTAGTGATGATGAAATCAAG
GCATATTTCTCACAATTTGGAAATATTACTGAAATGGAAATGCCATTCGATAAGCAAAAG
AATCAACGTAAAGCTTTCTGCTTTATCACTTTTGACTCGGAAGCTGTTGTCAATGAATTA
TTAAAGTCTCCAAAACAAACAATCAGTGGAAAGGAAGTTGATGTCAAAAAAGCCACGCCA
AAACCAGATAATGCTCCAATGATGCAACGTGGTGGAGGACGAAATATGAGAGGTGGACGA
GGAGGACGCGGATTTCAAGGAAATTGGAACGGATATGGAGGTGGTTATGGCCAAAACGGC
TGGAACCAAGGCGGAGGCAGTTGGGGTGGAAACAACTATGACAATTATCAGGGTGGTTAT
GGTGGTAGTGGTGTTGATTATCAGGGTAACTATGGCGGATACAACAATTATGATTATGGA
AATTACGGCGGCAGCGGTGGCAATTATGGCGGAAACTACCAAGGTGGAAAACAAAGAGGT
GGTGGGCGTCAACAAAGACATCAACCATATTAAGCCATTTTTCTTGGATTAAGTAAAAAT
ACAAACAACTCATCCATCTCATTCACTCATTGAAATCCTTAATTGTATTTTTTGAACATA
AATTATAATATCGACCGTGTCTTCAAAATGAAAAAGAATATTAAACAATAGCAGCAAAAA
CCAATCAAGAAAAACTCTCATCAAATGTTGAATTTATATATGCGTATATAAAATTCTCAC
ATACCATCATCAACAATAAATAA
>g1159.t12 Gene=g1159 Length=310
MADVQEYDNGEQMQEDFQGQGDQSGDSNYQNGNGETQARDDDRKLFVGGLSWETTEKELR
DHFGQYGEIDSINVKTDPTTGRSRGFAFIVYKAADSIDKVVAAGDHIINNKKVDPKKAKA
RTGKIFVGGLIPEISDDEIKAYFSQFGNITEMEMPFDKQKNQRKAFCFITFDSEAVVNEL
LKSPKQTISGKEVDVKKATPKPDNAPMMQRGGGRNMRGGRGGRGFQGNWNGYGGGYGQNG
WNQGGGSWGGNNYDNYQGGYGGSGVDYQGNYGGYNNYDYGNYGGSGGNYGGNYQGGKQRG
GGRQQRHQPY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1159.t12 | CDD | cd12325 | RRM1_hnRNPA_hnRNPD_like | 45 | 116 | 9.49547E-37 |
| 7 | g1159.t12 | Gene3D | G3DSA:3.30.70.330 | - | 37 | 115 | 8.4E-25 |
| 8 | g1159.t12 | Gene3D | G3DSA:3.30.70.330 | - | 116 | 231 | 1.3E-21 |
| 13 | g1159.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 42 | - |
| 12 | g1159.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 11 | 35 | - |
| 15 | g1159.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 192 | 219 | - |
| 14 | g1159.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 290 | 310 | - |
| 3 | g1159.t12 | PANTHER | PTHR48033:SF8 | RNA-BINDING PROTEIN SQUID | 9 | 310 | 6.6E-111 |
| 4 | g1159.t12 | PANTHER | PTHR48033 | RNA-BINDING (RRM/RBD/RNP MOTIFS) FAMILY PROTEIN | 9 | 310 | 6.6E-111 |
| 2 | g1159.t12 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 45 | 111 | 3.4E-17 |
| 1 | g1159.t12 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 125 | 192 | 3.8E-12 |
| 16 | g1159.t12 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 43 | 125 | 17.097 |
| 17 | g1159.t12 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 123 | 200 | 14.812 |
| 11 | g1159.t12 | SMART | SM00360 | rrm1_1 | 44 | 116 | 8.1E-24 |
| 10 | g1159.t12 | SMART | SM00360 | rrm1_1 | 124 | 196 | 2.2E-16 |
| 5 | g1159.t12 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 40 | 122 | 9.0E-25 |
| 6 | g1159.t12 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 113 | 215 | 3.12E-19 |
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 transcript has been annotated with K03102 (squid)
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.
