General information for g10830.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein lin-9-like protein.
Parent gene
- The parent gene g10830 is located on chr_1: 12167077..12170080 (- 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 | g10830 | g10830.t1 | TTS | g10830.t1 | 12165163 | 12165163 |
| chr_1 | g10830 | g10830.t1 | isoform | g10830.t1 | 12165469 | 12167388 |
| chr_1 | g10830 | g10830.t1 | exon | g10830.t1.exon1 | 12165469 | 12167388 |
| chr_1 | g10830 | g10830.t1 | cds | g10830.t1.CDS1 | 12165469 | 12167388 |
| chr_1 | g10830 | g10830.t1 | TSS | g10830.t1 | 12167846 | 12167846 |
Sequences
>g10830.t1 Gene=g10830 Length=1920
ATGTCTGACGACTCAAAGCGTGATGATTCACTAGAATCAACTGAAGAAGAAGAAGATGAG
TCATTTGGTCCAGCAGCACTTGGATTGCATCGTGTTGGTACAGAATTGCCAAAAAAGAAA
AAAAACTCACCTTTACAGAAACTCAATGCTCGTGGTCGTCCAGCTCGTATTCGGAAGAAA
AATTCAAAGTATGATGATGAACTTGAAGAGGCCAAAACGCCAACAAAGGTGTCTCCAATG
AAAAAAGTAACAAAAACTCCTACCACACAATCACCTATGAAAGTGACTGTTAAATCAGAA
AAGAAAACTTACAAAGGACGAAAATCGATGCACCACGATGATGATGATGATGACGACGAG
GAGGATGATGAAGAAGAAGAAAATTACGAAGAGAGTTCAGAATCGGGAAAAGCTGCAGTT
GTTCAAAAACCAATGGCCAAACGTGGGCCAAAAAAGAAGACTATCAAGTCATCAAGTTTC
ACTGAATCATCAAATATGAATAATATTGACAAGAAAGCATGCCAAAGAATCGGTTTGCGC
TTAAGAAATTTGCTTAAACTTCCCAAAGCTCATAAATTTGTCATGTATGAATTCTTCTAC
AGTAACATCGATCGAGCAATTTTCTTGGGAGCAAATGATTTTGATATTTGTATTTCAAAC
ACTTATCCTCGACTCAAGACACGCTTAATGACACGCATTGAATGGAATAAATTAAGACGA
TCATTTGGTAAGCCGAGACGTTGCTCAGCAAAATTTTTCGAAGAAGAGCGTATGGAGTTA
GAACGAAAACGTCAAAAGATTCGTTTATTGCAATCAAGAAAGACTGGTGACACTTCTTTT
GTTTATGATTTACCACCTGAAATTCCCGTTCCATTTACAATTGGAACAAAAGTTACTGCT
CGATTGAGGACACCACAAGATGGATTATTCACTGGAACTGTTGATGGTTTAGTTCATAAA
AGTCATTCTTATCGAATTGTGTTTGAACGACAAGGTATTGGCTCACAAGAAATTCCTGAT
TATGAAGTTATGGCATCTGAACCTCCTGATACGTTAGAAATTGAAAAAGTTACAAAAGAA
TTCGTATCACGACCTGATATTTCCTATTATATGGTGTCACCTCTTAAACCAGCTGGTGCA
TTCTCTTCATTCAGTGGTATAAGCAGTTTTCATAGAGGAGATCCTATGCTTTCATCTAGC
GGCAGTAATTTTATCAAACTTGAAGGATATCAAAAACCAAAATTACCTACACTTGTGCTC
CCAACGACAGGATCGATCGGTGGATATCCTATTAAATTACTAGAAACTATGGTTTTAGTA
AGAAAAACACTTGAAATCAAACACTTGCAATTGCTTAAGATTCGTCGTTTAAATGTTGAA
GCTGAAGTTGTAAAATCGTTTGGTGATAATGCACCTGAAGATTTCCAGAAAAAATATGCA
ACATTATTGATTGAAATGGAAAGAATCAATCGCGATTTGGCAGATTATATGAATATTCTA
CAAGCACAAACTGATTCATTCATTACAGACAAAGAAGAACTTGAAACAATCACACCAACA
TATTTGAGAGAAAAATGTCGGGATTTGGCAATGCAAACATTTGCAAAGAATAACAACAAC
GCCATTCAGGATGATGCAATGATTAAATTGATAGGAAATTTAGCCACAATTATGTGGGCT
ACTTCAAATCTTAAAAATGATCAATACACAAATGTCGAGGAAGTACTAAGTGGATGTCTC
ATTGAAACAAGCAAGACATTAGATGAAGAAAATCAAGCACTTTTCGAAAAGAGTGTTCAG
AGTCATATACATCAAATACAAATTGGAATTTTTGATGATAACTCAAATCAACCTCAGCCA
CAAGAAATCGAGGTATTGGAAGAAGAAGAAGTCGATGATGACTATGTGCTTGGAATTTAA
>g10830.t1 Gene=g10830 Length=639
MSDDSKRDDSLESTEEEEDESFGPAALGLHRVGTELPKKKKNSPLQKLNARGRPARIRKK
NSKYDDELEEAKTPTKVSPMKKVTKTPTTQSPMKVTVKSEKKTYKGRKSMHHDDDDDDDE
EDDEEEENYEESSESGKAAVVQKPMAKRGPKKKTIKSSSFTESSNMNNIDKKACQRIGLR
LRNLLKLPKAHKFVMYEFFYSNIDRAIFLGANDFDICISNTYPRLKTRLMTRIEWNKLRR
SFGKPRRCSAKFFEEERMELERKRQKIRLLQSRKTGDTSFVYDLPPEIPVPFTIGTKVTA
RLRTPQDGLFTGTVDGLVHKSHSYRIVFERQGIGSQEIPDYEVMASEPPDTLEIEKVTKE
FVSRPDISYYMVSPLKPAGAFSSFSGISSFHRGDPMLSSSGSNFIKLEGYQKPKLPTLVL
PTTGSIGGYPIKLLETMVLVRKTLEIKHLQLLKIRRLNVEAEVVKSFGDNAPEDFQKKYA
TLLIEMERINRDLADYMNILQAQTDSFITDKEELETITPTYLREKCRDLAMQTFAKNNNN
AIQDDAMIKLIGNLATIMWATSNLKNDQYTNVEEVLSGCLIETSKTLDEENQALFEKSVQ
SHIHQIQIGIFDDNSNQPQPQEIEVLEEEEVDDDYVLGI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g10830.t1 | Coils | Coil | Coil | 250 | 273 | - |
| 6 | g10830.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 163 | - |
| 9 | g10830.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 59 | 76 | - |
| 8 | g10830.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 79 | 97 | - |
| 7 | g10830.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 98 | 114 | - |
| 5 | g10830.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 115 | 131 | - |
| 2 | g10830.t1 | PANTHER | PTHR21689 | LIN-9 | 21 | 610 | 1.8E-95 |
| 3 | g10830.t1 | PANTHER | PTHR21689:SF2 | PROTEIN LIN-9 HOMOLOG | 21 | 610 | 1.8E-95 |
| 1 | g10830.t1 | Pfam | PF06584 | DIRP | 199 | 303 | 4.0E-39 |
| 4 | g10830.t1 | SMART | SM01135 | DIRP_2 | 199 | 304 | 1.2E-57 |
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:0017053 | transcription repressor complex | CC |
| GO:0006351 | transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K21773 (protein lin-9)
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.
