General information for g5184.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Heterogeneous nuclear ribonucleoprotein 27C.
Parent gene
- The parent gene g5184 is located on chr_2: 7564035..7564937 (- 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 | g5184 | g5184.t1 | isoform | g5184.t1 | 7564035 | 7564937 |
| chr_2 | g5184 | g5184.t1 | exon | g5184.t1.exon1 | 7564035 | 7564206 |
| chr_2 | g5184 | g5184.t1 | cds | g5184.t1.CDS1 | 7564035 | 7564206 |
| chr_2 | g5184 | g5184.t1 | exon | g5184.t1.exon2 | 7564366 | 7564403 |
| chr_2 | g5184 | g5184.t1 | cds | g5184.t1.CDS2 | 7564366 | 7564403 |
| chr_2 | g5184 | g5184.t1 | exon | g5184.t1.exon3 | 7564475 | 7564508 |
| chr_2 | g5184 | g5184.t1 | cds | g5184.t1.CDS3 | 7564475 | 7564508 |
| chr_2 | g5184 | g5184.t1 | exon | g5184.t1.exon4 | 7564591 | 7564722 |
| chr_2 | g5184 | g5184.t1 | cds | g5184.t1.CDS4 | 7564591 | 7564722 |
| chr_2 | g5184 | g5184.t1 | exon | g5184.t1.exon5 | 7564894 | 7564937 |
| chr_2 | g5184 | g5184.t1 | cds | g5184.t1.CDS5 | 7564894 | 7564937 |
| chr_2 | g5184 | g5184.t1 | TSS | g5184.t1 | NA | NA |
| chr_2 | g5184 | g5184.t1 | TTS | g5184.t1 | NA | NA |
Sequences
>g5184.t1 Gene=g5184 Length=420
ATGCGTATGAATGCCGGTGTCGATGTGGAGGATGATGAAAAGGGGAAGCTTTTTGTCGGT
GGGCTTGAGCTGGGAAACGACACAGGATTCATTGCAACGCTATTTCAGCCGATATGGCGA
AGTTATCGATTGTGTGGTGATGAAAATAATGAAACGGGAAGATCTAGAGGCTTTGGCTTT
GTGACTTTTGCTGATCAAAACAATGTGCAGGTCGTTTTGCAATCAGGTCCTCATAATTTG
GATGGAAGAACCATTGACCCAAAACAATGTAATCCAAGAACTATGCAGAAACCCAAGACA
CGCGGTGGCTCGTTTCCAAAAGTGTTTCTTGGTGGTCTACCATCGAATGTCACGGAAACC
GATTTACGAATGTATTTTGGGCGTTATGGGAAGTCATGGAAGTTGTCATCATGTATATGA
>g5184.t1 Gene=g5184 Length=139
MRMNAGVDVEDDEKGKLFVGGLELGNDTGFIATLFQPIWRSYRLCGDENNETGRSRGFGF
VTFADQNNVQVVLQSGPHNLDGRTIDPKQCNPRTMQKPKTRGGSFPKVFLGGLPSNVTET
DLRMYFGRYGKSWKLSSCI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5184.t1 | Gene3D | G3DSA:3.30.70.330 | - | 6 | 104 | 0.0000000 |
| 7 | g5184.t1 | Gene3D | G3DSA:3.30.70.330 | - | 105 | 138 | 0.0000330 |
| 2 | g5184.t1 | PANTHER | PTHR48027:SF12 | DAZ-ASSOCIATED PROTEIN 1 | 8 | 131 | 0.0000000 |
| 3 | g5184.t1 | PANTHER | PTHR48027 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED | 8 | 131 | 0.0000000 |
| 1 | g5184.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 40 | 85 | 0.0000190 |
| 8 | g5184.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 15 | 102 | 10.5820000 |
| 5 | g5184.t1 | SMART | SM00360 | rrm1_1 | 16 | 88 | 0.0000016 |
| 4 | g5184.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 13 | 131 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5184/g5184.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5184.t1.fa.iupred3.txt does not exist
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. There were no conditions that were differentially expressed