General information for g12532.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA primase large subunit.
Parent gene
- The parent gene g12532 is located on chr_1: 24276271..24278099 (+ 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 | g12532 | g12532.t2 | TSS | g12532.t2 | 24274489 | 24274489 |
| chr_1 | g12532 | g12532.t2 | isoform | g12532.t2 | 24274555 | 24276271 |
| chr_1 | g12532 | g12532.t2 | exon | g12532.t2.exon1 | 24274555 | 24274937 |
| chr_1 | g12532 | g12532.t2 | exon | g12532.t2.exon2 | 24274982 | 24276271 |
| chr_1 | g12532 | g12532.t2 | cds | g12532.t2.CDS1 | 24275009 | 24276271 |
| chr_1 | g12532 | g12532.t2 | TTS | g12532.t2 | 24276383 | 24276383 |
Sequences
>g12532.t2 Gene=g12532 Length=1673
ATGGATTTTACTAAACGAAGCAGGATTAAGTTATTAAAATCACCAGATGAAGACTCAATC
GATCGATTTGCACCACACAATTGCATGTTTTATATTTTACCACCTCAAAATGATGTAAGT
TTAAAAGATTTTGAGGACCTTGCAATTGAAAGATTAAAATTACTGAGAATTCTTGAGCAA
GCATCTTTGAAATATCCAAAGATTTTATCAGATGAATGGAAGGAATTTATTATAAATGAG
TTAAATGCAGAAGGTCTTAAATATTTTGTTCGATTAATAAAAGGCAATGGAAATTCAGAG
CAAGATAAACATGCTCGAAGAAGAGATTATCTTTCTCACTTCATTTTACGTTTTGCTTAT
TGTCGCAGTGAGGAATTAAGAAGTTTTTTAGATGGTTCATAACAAGAGAAATGGAATTGT
TTAAATTCAAATTTAGTTCATTGAGTTCTAATGAAATTAAAGATTTTATCGAACTATATG
AAATGGGATATCGACCGATTACTGATGAACAGAAAAATGAAGTACGTCAAGAATTACAAT
GCTCTTCAACAGGAAACATTGACACTATAGACTTTTATAAAGTGAATTTCTTGCAAGTTC
TTGATCTCGTTCGACAAAGAAAATGCTTTTTAAAAGGTGGATTTGCCTATGTGAGTTCTA
ATGATTTTAGCTCTATCATTGGTGGTCATCATCAGCAATTTATTGAGAAAGGTTTATTGT
CACATTTAAAATTGCTCCCAGAATTTGAGAATGATGAAAGAATAGTTGGAATAATAAAAG
GTTTACATACATCGTATGTTGGTAAAGATTATACAGTGAACAAAGATGCTGATGTTCCTA
TTGAAAGCTTAGATCAACTTTCACTCAAGTCTTATCCACTTTGTATGCGAATGTGTCATG
AATCGTTAAGAAAAACTCATCATTTAAAGCATTCTGGTCGTTTGCAGTATGGTCTGTTTT
TAAAAGGAATTGGTGTTTCATTGGAAGATTCACTCCGATTTTGGCGTGAAGAAATGACTA
AGAATATGGAAGTAGATAAATTTGATAAAAGTTATGCATATGGTATTCGATATAATTATG
GAAAGGAAGGATCAAGAACAAACTGGACTCCTTGGTCATGTGCCAAAATTATTTCAACCG
CTCCAGGTGCTCAAGACGTTGCTGGTTGTCCATTTAAATTATGGGATTCAATTGAGCTAA
AATCAAAATTAACAAGTTTTGGTCTCAATCCTATGGCAGTTCAGGATGTTGTGAGTTATG
CTAGTAAAGGACATTTTCAATTAGCTTGTGGACGTTATTTCGAGTCAGTACATGAAACTA
GACTTGATGAAGGTGTTAATCATCCAAATGGTTACTTTGAAAATAGTCAAATAATAATGG
GCAACAGGCAGACAAAAGAAAAGAATAAACCTTCTTCACAACAGTCCAATTTTAATCATC
GTAAGCAAGTTCAGATGAACAAACAACAAGAATTCAAACGTAAAATGGACATAAAAATTA
AAGAAGAAAAAGATTTTGATGAAGAGCTGTGGAAATTATCACAACGTGAGGAGGAATTAT
TGAATGAATGGAATACACGACAAGAGCAAACTAAAAAAGAAGTTGCTGAAATTTCTCAAA
TGGATTGGAATGATGATGATGAAGACATGTCTCAAATTAATAATTATTTGTAA
>g12532.t2 Gene=g12532 Length=420
MELFKFKFSSLSSNEIKDFIELYEMGYRPITDEQKNEVRQELQCSSTGNIDTIDFYKVNF
LQVLDLVRQRKCFLKGGFAYVSSNDFSSIIGGHHQQFIEKGLLSHLKLLPEFENDERIVG
IIKGLHTSYVGKDYTVNKDADVPIESLDQLSLKSYPLCMRMCHESLRKTHHLKHSGRLQY
GLFLKGIGVSLEDSLRFWREEMTKNMEVDKFDKSYAYGIRYNYGKEGSRTNWTPWSCAKI
ISTAPGAQDVAGCPFKLWDSIELKSKLTSFGLNPMAVQDVVSYASKGHFQLACGRYFESV
HETRLDEGVNHPNGYFENSQIIMGNRQTKEKNKPSSQQSNFNHRKQVQMNKQQEFKRKMD
IKIKEEKDFDEELWKLSQREEELLNEWNTRQEQTKKEVAEISQMDWNDDDEDMSQINNYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12532.t2 | CDD | cd07322 | PriL_PriS_Eukaryotic | 1 | 319 | 2.00227E-140 |
| 7 | g12532.t2 | Coils | Coil | Coil | 377 | 397 | - |
| 6 | g12532.t2 | Gene3D | G3DSA:1.20.930.80 | - | 1 | 125 | 3.6E-31 |
| 4 | g12532.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 327 | 348 | - |
| 5 | g12532.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 327 | 353 | - |
| 2 | g12532.t2 | PANTHER | PTHR10537 | DNA PRIMASE LARGE SUBUNIT | 1 | 354 | 5.6E-109 |
| 3 | g12532.t2 | PANTHER | PTHR10537:SF3 | DNA PRIMASE LARGE SUBUNIT | 1 | 354 | 5.6E-109 |
| 1 | g12532.t2 | Pfam | PF04104 | Eukaryotic and archaeal DNA primase, large subunit | 54 | 316 | 5.0E-77 |
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:0006269 | DNA replication, synthesis of RNA primer | BP |
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.
