General information for g10979.t10
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.t10 | isoform | g10979.t10 | 13113171 | 13114703 |
| chr_1 | g10979 | g10979.t10 | exon | g10979.t10.exon1 | 13113171 | 13113887 |
| chr_1 | g10979 | g10979.t10 | cds | g10979.t10.CDS1 | 13113171 | 13113887 |
| chr_1 | g10979 | g10979.t10 | exon | g10979.t10.exon2 | 13113969 | 13114251 |
| chr_1 | g10979 | g10979.t10 | cds | g10979.t10.CDS2 | 13113969 | 13114251 |
| chr_1 | g10979 | g10979.t10 | exon | g10979.t10.exon3 | 13114318 | 13114432 |
| chr_1 | g10979 | g10979.t10 | cds | g10979.t10.CDS3 | 13114318 | 13114355 |
| chr_1 | g10979 | g10979.t10 | exon | g10979.t10.exon4 | 13114665 | 13114703 |
| chr_1 | g10979 | g10979.t10 | TSS | g10979.t10 | 13114799 | 13114799 |
| chr_1 | g10979 | g10979.t10 | TTS | g10979.t10 | NA | NA |
Sequences
>g10979.t10 Gene=g10979 Length=1154
ATGATTTCTCAAAAGGATAACGAAGAAGGGAAATTGTTTGCCTGAGCTGGGATACTCAGT
CGGATAGTCTACAACGTTATTTTAGCCGCTATGGTGAAGTTATTGATTGTGTTGTAATGA
AAAACAATGAAACAGGCAGATCAAGAGGATTCGGTTTTGTGACTTTTGCTGATCCTGAGA
ATGTAAAGCGCGCTCTTGACAATTGCCCTCATAGTTTGGACGGAAGGACGATCGATCCAA
AACCATGTAATCCTCGCTCGATGCATAAACCGAAGCGAACTAATGCTGGGTATCCGAAAG
TCTTTCTCGGTGGTTTGCCTGCGAACGTTACCGAGTCCGATTTGAGAGCATATTTCTCTC
GTTATGGACAGGTAATGGAAGTGGTCATAATGTACGATCAAGAGAAAAAGAAGAGTCGTG
GTTTTGGTTTTCTATCGTTCGATTATGTAAAGTTTGATACTGAAGCATCTGTGGATAGAG
CTTGTGCAGATCACTTCATTAATCTTAATGGTAAGCAAGTTGAAATTAAGAAAGCTGAAC
CAAGAGATGGTTCAAATCATATGATGCAAATGGATCCAAGTCAATCGATTGGAGCATCGC
ATTGGGGAGGGCCAATGATGAGTGGAAATGGACCAATGATGGGACCGATTAGTGTTCCAA
ATTTGGCAGGAAATACTGGCTTCAATTATAATTATGGATCATCAAATCCTTCAGCTAATC
CCAACTTTGGATGGCCTCAACAATGGGGTAATACGGGAAATTACGGAGTTCCTCATCAAG
CTCAACAATCGGCTCAAGGCTACGGAGCTGCAGCTGCTTATGATTATAATGGTCCAATCG
GATATAACTCGACACCAAGCAGTTATGCAGCAGCTAATGGTAACAATTGGAATTCTTGGA
ATCCAAACATTACAAACATCGCCCCAAATACTGGATCATCATCAGGAGAACTTCAATATC
GACCACAATCTGGGCCAAATATGCATTCAGGTCCACCACCGCCGACATCAGGAAGTCTCT
CAAAAGCAGGCTCTGAATACAACGGAGCCGCGGCATATAATGGTGCAGCATACACAAATT
ACTATAATGAGCAACAGTTTAGTAATCAAAATCGACCACGTTCGTACGGTAACGAGCAAT
ATCCAGCTTTTTAA
>g10979.t10 Gene=g10979 Length=345
MKNNETGRSRGFGFVTFADPENVKRALDNCPHSLDGRTIDPKPCNPRSMHKPKRTNAGYP
KVFLGGLPANVTESDLRAYFSRYGQVMEVVIMYDQEKKKSRGFGFLSFDYVKFDTEASVD
RACADHFINLNGKQVEIKKAEPRDGSNHMMQMDPSQSIGASHWGGPMMSGNGPMMGPISV
PNLAGNTGFNYNYGSSNPSANPNFGWPQQWGNTGNYGVPHQAQQSAQGYGAAAAYDYNGP
IGYNSTPSSYAAANGNNWNSWNPNITNIAPNTGSSSGELQYRPQSGPNMHSGPPPPTSGS
LSKAGSEYNGAAAYNGAAYTNYYNEQQFSNQNRPRSYGNEQYPAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g10979.t10 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 59 | 2.2E-11 |
| 9 | g10979.t10 | Gene3D | G3DSA:3.30.70.330 | - | 60 | 144 | 2.9E-22 |
| 7 | g10979.t10 | MobiDBLite | mobidb-lite | consensus disorder prediction | 325 | 345 | - |
| 3 | g10979.t10 | PANTHER | PTHR48027:SF12 | DAZ-ASSOCIATED PROTEIN 1 | 1 | 340 | 2.7E-67 |
| 4 | g10979.t10 | PANTHER | PTHR48027 | HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN 87F-RELATED | 1 | 340 | 2.7E-67 |
| 1 | g10979.t10 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 3 | 32 | 6.4E-7 |
| 2 | g10979.t10 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 62 | 110 | 1.9E-13 |
| 11 | g10979.t10 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 49 | 9.951 |
| 10 | g10979.t10 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 60 | 142 | 16.023 |
| 6 | g10979.t10 | SMART | SM00360 | rrm1_1 | 61 | 138 | 7.0E-18 |
| 5 | g10979.t10 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 109 | 1.01E-29 |
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: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