General information for g10979.t1
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 g10979 is located on chr_1: 13113311..13114703 (- 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_1 | g10979 | g10979.t1 | isoform | g10979.t1 | 13113171 | 13114703 |
| chr_1 | g10979 | g10979.t1 | exon | g10979.t1.exon1 | 13113171 | 13113872 |
| chr_1 | g10979 | g10979.t1 | cds | g10979.t1.CDS1 | 13113171 | 13113872 |
| chr_1 | g10979 | g10979.t1 | exon | g10979.t1.exon2 | 13113969 | 13114251 |
| chr_1 | g10979 | g10979.t1 | cds | g10979.t1.CDS2 | 13113969 | 13114251 |
| chr_1 | g10979 | g10979.t1 | exon | g10979.t1.exon3 | 13114318 | 13114432 |
| chr_1 | g10979 | g10979.t1 | cds | g10979.t1.CDS3 | 13114318 | 13114432 |
| chr_1 | g10979 | g10979.t1 | exon | g10979.t1.exon4 | 13114658 | 13114703 |
| chr_1 | g10979 | g10979.t1 | cds | g10979.t1.CDS4 | 13114658 | 13114703 |
| chr_1 | g10979 | g10979.t1 | TSS | g10979.t1 | 13114799 | 13114799 |
| chr_1 | g10979 | g10979.t1 | TTS | g10979.t1 | NA | NA |
Sequences
>g10979.t1 Gene=g10979 Length=1146
ATGATTTCTCAAAAGGATAACGAAGAAGGGAAATTGTTTGTAGGCGGCCTGAGCTGGGAT
ACTCAGTCGGATAGTCTACAACGTTATTTTAGCCGCTATGGTGAAGTTATTGATTGTGTT
GTAATGAAAAACAATGAAACAGGCAGATCAAGAGGATTCGGTTTTGTGACTTTTGCTGAT
CCTGAGAATGTAAAGCGCGCTCTTGACAATTGCCCTCATAGTTTGGACGGAAGGACGATC
GATCCAAAACCATGTAATCCTCGCTCGATGCATAAACCGAAGCGAACTAATGCTGGGTAT
CCGAAAGTCTTTCTCGGTGGTTTGCCTGCGAACGTTACCGAGTCCGATTTGAGAGCATAT
TTCTCTCGTTATGGACAGGTAATGGAAGTGGTCATAATGTACGATCAAGAGAAAAAGAAG
AGTCGTGGTTTTGGTTTTCTATCGTTTGATACTGAAGCATCTGTGGATAGAGCTTGTGCA
GATCACTTCATTAATCTTAATGGTAAGCAAGTTGAAATTAAGAAAGCTGAACCAAGAGAT
GGTTCAAATCATATGATGCAAATGGATCCAAGTCAATCGATTGGAGCATCGCATTGGGGA
GGGCCAATGATGAGTGGAAATGGACCAATGATGGGACCGATTAGTGTTCCAAATTTGGCA
GGAAATACTGGCTTCAATTATAATTATGGATCATCAAATCCTTCAGCTAATCCCAACTTT
GGATGGCCTCAACAATGGGGTAATACGGGAAATTACGGAGTTCCTCATCAAGCTCAACAA
TCGGCTCAAGGCTACGGAGCTGCAGCTGCTTATGATTATAATGGTCCAATCGGATATAAC
TCGACACCAAGCAGTTATGCAGCAGCTAATGGTAACAATTGGAATTCTTGGAATCCAAAC
ATTACAAACATCGCCCCAAATACTGGATCATCATCAGGAGAACTTCAATATCGACCACAA
TCTGGGCCAAATATGCATTCAGGTCCACCACCGCCGACATCAGGAAGTCTCTCAAAAGCA
GGCTCTGAATACAACGGAGCCGCGGCATATAATGGTGCAGCATACACAAATTACTATAAT
GAGCAACAGTTTAGTAATCAAAATCGACCACGTTCGTACGGTAACGAGCAATATCCAGCT
TTTTAA
>g10979.t1 Gene=g10979 Length=381
MISQKDNEEGKLFVGGLSWDTQSDSLQRYFSRYGEVIDCVVMKNNETGRSRGFGFVTFAD
PENVKRALDNCPHSLDGRTIDPKPCNPRSMHKPKRTNAGYPKVFLGGLPANVTESDLRAY
FSRYGQVMEVVIMYDQEKKKSRGFGFLSFDTEASVDRACADHFINLNGKQVEIKKAEPRD
GSNHMMQMDPSQSIGASHWGGPMMSGNGPMMGPISVPNLAGNTGFNYNYGSSNPSANPNF
GWPQQWGNTGNYGVPHQAQQSAQGYGAAAAYDYNGPIGYNSTPSSYAAANGNNWNSWNPN
ITNIAPNTGSSSGELQYRPQSGPNMHSGPPPPTSGSLSKAGSEYNGAAAYNGAAYTNYYN
EQQFSNQNRPRSYGNEQYPAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g10979.t1 | CDD | cd12327 | RRM2_DAZAP1 | 99 | 178 | 0.000 |
| 10 | g10979.t1 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 96 | 0.000 |
| 9 | g10979.t1 | Gene3D | G3DSA:3.30.70.330 | - | 101 | 180 | 0.000 |
| 3 | g10979.t1 | PANTHER | PTHR48027:SF12 | DAZ-ASSOCIATED PROTEIN 1 | 5 | 376 | 0.000 |
| 4 | g10979.t1 | PANTHER | PTHR48027 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED | 5 | 376 | 0.000 |
| 2 | g10979.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 12 | 73 | 0.000 |
| 1 | g10979.t1 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 103 | 169 | 0.000 |
| 12 | g10979.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 10 | 90 | 18.001 |
| 11 | g10979.t1 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 101 | 178 | 18.325 |
| 7 | g10979.t1 | SMART | SM00360 | rrm1_1 | 11 | 83 | 0.000 |
| 8 | g10979.t1 | SMART | SM00360 | rrm1_1 | 102 | 174 | 0.000 |
| 6 | g10979.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 9 | 95 | 0.000 |
| 5 | g10979.t1 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 99 | 188 | 0.000 |
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:0003723 | RNA binding | MF |
| GO:0003676 | nucleic acid binding | MF |
KEGG
Orthology
- This transcript has been annotated with K14411 (RNA-binding protein Musashi)
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.
