General information for g5178.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Heterogeneous nuclear ribonucleoprotein 27C.
Parent gene
- The parent gene g5178 is located on chr_2: 7551462..7552876 (- 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 | g5178 | g5178.t4 | TTS | g5178.t4 | 7550278 | 7550278 |
| chr_2 | g5178 | g5178.t4 | isoform | g5178.t4 | 7551294 | 7552876 |
| chr_2 | g5178 | g5178.t4 | exon | g5178.t4.exon1 | 7551294 | 7551392 |
| chr_2 | g5178 | g5178.t4 | cds | g5178.t4.CDS1 | 7551295 | 7551392 |
| chr_2 | g5178 | g5178.t4 | exon | g5178.t4.exon2 | 7551463 | 7552142 |
| chr_2 | g5178 | g5178.t4 | cds | g5178.t4.CDS2 | 7551463 | 7552142 |
| chr_2 | g5178 | g5178.t4 | exon | g5178.t4.exon3 | 7552301 | 7552338 |
| chr_2 | g5178 | g5178.t4 | cds | g5178.t4.CDS3 | 7552301 | 7552338 |
| chr_2 | g5178 | g5178.t4 | exon | g5178.t4.exon4 | 7552413 | 7552446 |
| chr_2 | g5178 | g5178.t4 | cds | g5178.t4.CDS4 | 7552413 | 7552446 |
| chr_2 | g5178 | g5178.t4 | exon | g5178.t4.exon5 | 7552529 | 7552876 |
| chr_2 | g5178 | g5178.t4 | cds | g5178.t4.CDS5 | 7552529 | 7552566 |
| chr_2 | g5178 | g5178.t4 | TSS | g5178.t4 | 7552986 | 7552986 |
Sequences
>g5178.t4 Gene=g5178 Length=1199
ATGCGTATGAATGCCGGTGTCGATGTGGAGGATGATGAAAAGGGGTAAGAGTAGCACAAA
ATTTTAAATGAAAAAATTGGATCTCATTTTTGATGATGTGACAAAATTTTGCAAAAAAAG
TGAGAGAGAGGAAGAAAAAAATGAGAAAATGGTTTAATTTGATTTGATCGCATACTTTTT
CCTTGTCTCATGTCATGTTTTATTTGTACAAAATAGGAAGCTTTTTGTCGGTGGCTTGAG
CTGGGAAACGACACAGGATTCATTGCAACGCTATTTCAGCCGATATGGCGAAGTTATCGA
TTGTGTGGTGATGAAAAATAATGAAACGGGAAGATCTAGAGGCTTTGGCTTTGTGACTTT
TGCTGATCCAAACAATGTGCAGGTCGTTTTGCAATCAGGTCCTCATAATTTGGATGGAAG
AACCATTGACCCAAAACAATGTAATCCAAGAACTATGCAGAAACCCAAGACACGCGGTGG
CTCGTTTCCAAAAGTGTTTCTTGGTGGTCTACCATCGAATGTCACGGAAACCGATTTACG
AATGTATTTTGGGCGTTATGGGAAAGTCATGGAAGTTGTCATCATGTATGATCAAGAGAA
GAAAAAGTCTCGTGGCTTTGGTTTCTTGTCATTTGAGGATGATGCATCAGTTGAACGTGT
TTGTACTGAGCATTACATTACATTGAATGGAAAGCAGGTCGAGATAAAGAAAGCTGAGCC
GAGAGATGGTTCGACAAATCATAAAATGAGTCAGGATGCAATTCAATCGATGGGCTCAAA
TTCGAGTTGGGGTCCTCCTGGTGGACAAATGCCAAGCAGTGGAGTTAATCCAATGATGCA
AGGTCCAAATGGGCAAATGAATGCTCCTCAACACATGAATATGATGGCTCCAAATATGCT
TGGTGGTTATCCATCAAGTTGGAATTCACAACAACAGAGCTATGGCTATAGTGGTGCACC
AAATCATGCGGGTGCATATAATCAACAAAATTGGGGACCTGCACAAGCTCCTCAAGCGGG
TCCACCACCGCCAGCAATGGGACAATGGGGAAATTATAATGCTGCCACACCACAAACACA
AGGCTACAATTCATCTTATGACATGTATAACTCATCGACTGGTCCATCTGCAGGATCTGG
AGGCAATTGGAATTCATGGGGACCGCTAACTAATTCCGGCGCAACTAATGCCGGATCTA
>g5178.t4 Gene=g5178 Length=296
MKNNETGRSRGFGFVTFADPNNVQVVLQSGPHNLDGRTIDPKQCNPRTMQKPKTRGGSFP
KVFLGGLPSNVTETDLRMYFGRYGKVMEVVIMYDQEKKKSRGFGFLSFEDDASVERVCTE
HYITLNGKQVEIKKAEPRDGSTNHKMSQDAIQSMGSNSSWGPPGGQMPSSGVNPMMQGPN
GQMNAPQHMNMMAPNMLGGYPSSWNSQQQSYGYSGAPNHAGAYNQQNWGPAQAPQAGPPP
PAMGQWGNYNAATPQTQGYNSSYDMYNSSTGPSAGSGGNWNSWGPLTNSGATNAGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5178.t4 | CDD | cd12327 | RRM2_DAZAP1 | 60 | 137 | 1.01345E-46 |
| 7 | g5178.t4 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 59 | 6.9E-10 |
| 8 | g5178.t4 | Gene3D | G3DSA:3.30.70.330 | - | 60 | 139 | 2.4E-23 |
| 13 | g5178.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 134 | 164 | - |
| 12 | g5178.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 144 | 164 | - |
| 11 | g5178.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 270 | 296 | - |
| 3 | g5178.t4 | PANTHER | PTHR48027:SF12 | DAZ-ASSOCIATED PROTEIN 1 | 1 | 286 | 8.4E-75 |
| 4 | g5178.t4 | PANTHER | PTHR48027 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED | 1 | 286 | 8.4E-75 |
| 1 | g5178.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 3 | 39 | 1.6E-4 |
| 2 | g5178.t4 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 62 | 129 | 2.2E-15 |
| 14 | g5178.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 56 | 9.286 |
| 15 | g5178.t4 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 60 | 137 | 17.575 |
| 10 | g5178.t4 | SMART | SM00360 | rrm1_1 | 61 | 133 | 1.3E-22 |
| 5 | g5178.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 54 | 6.79E-10 |
| 6 | g5178.t4 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 59 | 164 | 5.51E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5178/g5178.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5178.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003723 | RNA binding | MF |
| 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.
