General information for g10979.t9
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.t9 | TTS | g10979.t9 | 13111795 | 13111795 |
| chr_1 | g10979 | g10979.t9 | isoform | g10979.t9 | 13112596 | 13114703 |
| chr_1 | g10979 | g10979.t9 | exon | g10979.t9.exon1 | 13112596 | 13113872 |
| chr_1 | g10979 | g10979.t9 | cds | g10979.t9.CDS1 | 13113171 | 13113872 |
| chr_1 | g10979 | g10979.t9 | exon | g10979.t9.exon2 | 13113969 | 13114251 |
| chr_1 | g10979 | g10979.t9 | cds | g10979.t9.CDS2 | 13113969 | 13114251 |
| chr_1 | g10979 | g10979.t9 | exon | g10979.t9.exon3 | 13114318 | 13114703 |
| chr_1 | g10979 | g10979.t9 | cds | g10979.t9.CDS3 | 13114318 | 13114355 |
| chr_1 | g10979 | g10979.t9 | TSS | g10979.t9 | 13114799 | 13114799 |
Sequences
>g10979.t9 Gene=g10979 Length=1946
ATGATTTCTCAAAAGGATAACGAAGAAGGGAAATTGTTTGTAGGCGGTAAGTGACTGGAT
TTTATTTATTTTTTTGCTATTTTACGGAAGCGCTTCACTATGATGCATTGTGGCGTTTTG
GCTGAGTACGGAAAAAGAGTAACCTTTCTCTCTCTCAAACAAAAAAAGAATAAGAAAGTG
TTTTTGTTTATTTTGGTCACACTGCAATTGCCGCGATATCATGAATTTATGTGATAAACA
CTAATCGCATTATTTTAAATCTATTTCTAAGGCCTGAGCTGGGATACTCAGTCGGATAGT
CTACAACGTTATTTTAGCCGCTATGGTGAAGTTATTGATTGTGTTGTAATGAAAAACAAT
GAAACAGGCAGATCAAGAGGATTCGGTTTTGTGACTTTTGCTGATCCTGAGAATGTAAAG
CGCGCTCTTGACAATTGCCCTCATAGTTTGGACGGAAGGACGATCGATCCAAAACCATGT
AATCCTCGCTCGATGCATAAACCGAAGCGAACTAATGCTGGGTATCCGAAAGTCTTTCTC
GGTGGTTTGCCTGCGAACGTTACCGAGTCCGATTTGAGAGCATATTTCTCTCGTTATGGA
CAGGTAATGGAAGTGGTCATAATGTACGATCAAGAGAAAAAGAAGAGTCGTGGTTTTGGT
TTTCTATCGTTTGATACTGAAGCATCTGTGGATAGAGCTTGTGCAGATCACTTCATTAAT
CTTAATGGTAAGCAAGTTGAAATTAAGAAAGCTGAACCAAGAGATGGTTCAAATCATATG
ATGCAAATGGATCCAAGTCAATCGATTGGAGCATCGCATTGGGGAGGGCCAATGATGAGT
GGAAATGGACCAATGATGGGACCGATTAGTGTTCCAAATTTGGCAGGAAATACTGGCTTC
AATTATAATTATGGATCATCAAATCCTTCAGCTAATCCCAACTTTGGATGGCCTCAACAA
TGGGGTAATACGGGAAATTACGGAGTTCCTCATCAAGCTCAACAATCGGCTCAAGGCTAC
GGAGCTGCAGCTGCTTATGATTATAATGGTCCAATCGGATATAACTCGACACCAAGCAGT
TATGCAGCAGCTAATGGTAACAATTGGAATTCTTGGAATCCAAACATTACAAACATCGCC
CCAAATACTGGATCATCATCAGGAGAACTTCAATATCGACCACAATCTGGGCCAAATATG
CATTCAGGTCCACCACCGCCGACATCAGGAAGTCTCTCAAAAGCAGGCTCTGAATACAAC
GGAGCCGCGGCATATAATGGTGCAGCATACACAAATTACTATAATGAGCAACAGTTTAGT
AATCAAAATCGACCACGTTCGTACGGTAACGAGCAATATCCAGCTTTTTAAGAGTACACA
AATGATTGCTTTTCGTCTTAATTTTTTATTATTTTATTCTTAAAGTTGACGTGCATTCTC
GCAGTGGATTATAAAATCAATTTCCTTCTGCTCTCGCCTGCTCCTCCCCTTCTTCGATCT
GGAGTTTCCCTACCTAATTCTTTTTAAAATGTAATTTATGTAGAAGCAATTTTAAACATA
TTTCTTTTATCCCAATTTTAACTACAACCTTTTTACCGTTCTGATTTTATCCATCCATAC
AATAATAGTAATGAAAAAAGTAACATCTTAACGTTAAAGGTCTCTACGAATACATAATTT
TAGAGTGACGATTTTAATTTTTACAATTACTGTACACACAATAACTTGAAAATTATTAAA
TGTATCATTTAGTTTTGATAGTATTTTAATGGATTTCGTCGAGATTACTCGATGGAGAAA
AAAAAGATATAACAGTTTTTATATTTTTTTCGATTATTCCGAATATTGTTGTTGATTCTT
CTTTTTTAAAAGAAAAAAAATTAAATCGTAAGGTGCGAAATAGAATTAAAATGAAAAACA
AAAATTAATCTTCGATTCTAATTAAA
>g10979.t9 Gene=g10979 Length=340
MKNNETGRSRGFGFVTFADPENVKRALDNCPHSLDGRTIDPKPCNPRSMHKPKRTNAGYP
KVFLGGLPANVTESDLRAYFSRYGQVMEVVIMYDQEKKKSRGFGFLSFDTEASVDRACAD
HFINLNGKQVEIKKAEPRDGSNHMMQMDPSQSIGASHWGGPMMSGNGPMMGPISVPNLAG
NTGFNYNYGSSNPSANPNFGWPQQWGNTGNYGVPHQAQQSAQGYGAAAAYDYNGPIGYNS
TPSSYAAANGNNWNSWNPNITNIAPNTGSSSGELQYRPQSGPNMHSGPPPPTSGSLSKAG
SEYNGAAAYNGAAYTNYYNEQQFSNQNRPRSYGNEQYPAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10979.t9 | CDD | cd12327 | RRM2_DAZAP1 | 58 | 137 | 1.08743E-46 |
| 7 | g10979.t9 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 59 | 2.2E-11 |
| 8 | g10979.t9 | Gene3D | G3DSA:3.30.70.330 | - | 60 | 139 | 5.3E-24 |
| 11 | g10979.t9 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 340 | - |
| 3 | g10979.t9 | PANTHER | PTHR48027:SF12 | DAZ-ASSOCIATED PROTEIN 1 | 1 | 335 | 6.1E-70 |
| 4 | g10979.t9 | PANTHER | PTHR48027 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED | 1 | 335 | 6.1E-70 |
| 1 | g10979.t9 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 3 | 32 | 6.3E-7 |
| 2 | g10979.t9 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 62 | 128 | 5.2E-16 |
| 13 | g10979.t9 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 49 | 9.951 |
| 12 | g10979.t9 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 60 | 137 | 18.325 |
| 10 | g10979.t9 | SMART | SM00360 | rrm1_1 | 61 | 133 | 9.1E-23 |
| 5 | g10979.t9 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 54 | 1.24E-11 |
| 6 | g10979.t9 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 58 | 148 | 7.93E-24 |
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 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.
