General information for g5178.t3
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 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.t3 | TTS | g5178.t3 | 7550278 | 7550278 |
| chr_2 | g5178 | g5178.t3 | isoform | g5178.t3 | 7551074 | 7552135 |
| chr_2 | g5178 | g5178.t3 | exon | g5178.t3.exon1 | 7551074 | 7551179 |
| chr_2 | g5178 | g5178.t3 | cds | g5178.t3.CDS1 | 7551076 | 7551179 |
| chr_2 | g5178 | g5178.t3 | exon | g5178.t3.exon2 | 7551294 | 7551392 |
| chr_2 | g5178 | g5178.t3 | cds | g5178.t3.CDS2 | 7551294 | 7551392 |
| chr_2 | g5178 | g5178.t3 | exon | g5178.t3.exon3 | 7551463 | 7552135 |
| chr_2 | g5178 | g5178.t3 | cds | g5178.t3.CDS3 | 7551463 | 7552108 |
| chr_2 | g5178 | g5178.t3 | TSS | g5178.t3 | 7552986 | 7552986 |
Sequences
>g5178.t3 Gene=g5178 Length=878
GACCCAAAACAATGTAATCCAAGAACTATGCAGAAACCCAAGACACGCGGTGGCTCGTTT
CCAAAAGTGTTTCTTGGTGGTCTACCATCGAATGTCACGGAAACCGATTTACGAATGTAT
TTTGGGCGTTATGGGAAAGTCATGGAAGTTGTCATCATGTATGATCAAGAGAAGAAAAAG
TCTCGTGGCTTTGGTTTCTTGTCATTTGAGGATGATGCATCAGTTGAACGTGTTTGTACT
GAGCATTACATTACATTGAATGGAAAGCAGGTCGAGATAAAGAAAGCTGAGCCGAGAGAT
GGTTCGACAAATCATAAAATGAGTCAGGATGCAATTCAATCGATGGGCTCAAATTCGAGT
TGGGGTCCTCCTGGTGGACAAATGCCAAGCAGTGGAGTTAATCCAATGATGCAAGGTCCA
AATGGGCAAATGAATGCTCCTCAACACATGAATATGATGGCTCCAAATATGCTTGGTGGT
TATCCATCAAGTTGGAATTCACAACAACAGAGCTATGGCTATAGTGGTGCACCAAATCAT
GCGGGTGCATATAATCAACAAAATTGGGGACCTGCACAAGCTCCTCAAGCGGGTCCACCA
CCGCCAGCAATGGGACAATGGGGAAATTATAATGCTGCCACACCACAAACACAAGGCTAC
AATTCATCTTATGACATGTATAACTCATCGACTGGTCCATCTGCAGGATCTGGAGGCAAT
TGGAATTCATGGGGACCGCTAACTAATTCCGGCGCAACTAATGCCGGATCTAATGACATG
TATAATCGTCAATCAAGCACGGCAGGACCTAATATGGGTCCACCACCGACCGCAACTGCT
AATAATAAACCTCCATCAGATTATTCGTACGGGAATTA
>g5178.t3 Gene=g5178 Length=283
MQKPKTRGGSFPKVFLGGLPSNVTETDLRMYFGRYGKVMEVVIMYDQEKKKSRGFGFLSF
EDDASVERVCTEHYITLNGKQVEIKKAEPRDGSTNHKMSQDAIQSMGSNSSWGPPGGQMP
SSGVNPMMQGPNGQMNAPQHMNMMAPNMLGGYPSSWNSQQQSYGYSGAPNHAGAYNQQNW
GPAQAPQAGPPPPAMGQWGNYNAATPQTQGYNSSYDMYNSSTGPSAGSGGNWNSWGPLTN
SGATNAGSNDMYNRQSSTAGPNMGPPPTATANNKPPSDYSYGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5178.t3 | CDD | cd12327 | RRM2_DAZAP1 | 12 | 89 | 6.97447E-47 |
| 5 | g5178.t3 | Gene3D | G3DSA:3.30.70.330 | - | 12 | 91 | 2.3E-23 |
| 9 | g5178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 86 | 116 | - |
| 8 | g5178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 116 | - |
| 10 | g5178.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 240 | 283 | - |
| 2 | g5178.t3 | PANTHER | PTHR48027:SF12 | DAZ-ASSOCIATED PROTEIN 1 | 12 | 282 | 3.0E-53 |
| 3 | g5178.t3 | PANTHER | PTHR48027 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED | 12 | 282 | 3.0E-53 |
| 1 | g5178.t3 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 14 | 81 | 2.0E-15 |
| 11 | g5178.t3 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 12 | 89 | 17.575 |
| 7 | g5178.t3 | SMART | SM00360 | rrm1_1 | 13 | 85 | 1.3E-22 |
| 4 | g5178.t3 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 12 | 116 | 5.24E-23 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5178/g5178.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5178.t3.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.
