General information for g12532.t1
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.t1 | TSS | g12532.t1 | 24274489 | 24274489 |
| chr_1 | g12532 | g12532.t1 | isoform | g12532.t1 | 24274555 | 24276271 |
| chr_1 | g12532 | g12532.t1 | exon | g12532.t1.exon1 | 24274555 | 24274937 |
| chr_1 | g12532 | g12532.t1 | cds | g12532.t1.CDS1 | 24274555 | 24274937 |
| chr_1 | g12532 | g12532.t1 | exon | g12532.t1.exon2 | 24274990 | 24276271 |
| chr_1 | g12532 | g12532.t1 | cds | g12532.t1.CDS2 | 24274990 | 24276271 |
| chr_1 | g12532 | g12532.t1 | TTS | g12532.t1 | 24276383 | 24276383 |
Sequences
>g12532.t1 Gene=g12532 Length=1665
ATGGATTTTACTAAACGAAGCAGGATTAAGTTATTAAAATCACCAGATGAAGACTCAATC
GATCGATTTGCACCACACAATTGCATGTTTTATATTTTACCACCTCAAAATGATGTAAGT
TTAAAAGATTTTGAGGACCTTGCAATTGAAAGATTAAAATTACTGAGAATTCTTGAGCAA
GCATCTTTGAAATATCCAAAGATTTTATCAGATGAATGGAAGGAATTTATTATAAATGAG
TTAAATGCAGAAGGTCTTAAATATTTTGTTCGATTAATAAAAGGCAATGGAAATTCAGAG
CAAGATAAACATGCTCGAAGAAGAGATTATCTTTCTCACTTCATTTTACGTTTTGCTTAT
TGTCGCAGTGAGGAATTAAGAAGATGGTTCATAACAAGAGAAATGGAATTGTTTAAATTC
AAATTTAGTTCATTGAGTTCTAATGAAATTAAAGATTTTATCGAACTATATGAAATGGGA
TATCGACCGATTACTGATGAACAGAAAAATGAAGTACGTCAAGAATTACAATGCTCTTCA
ACAGGAAACATTGACACTATAGACTTTTATAAAGTGAATTTCTTGCAAGTTCTTGATCTC
GTTCGACAAAGAAAATGCTTTTTAAAAGGTGGATTTGCCTATGTGAGTTCTAATGATTTT
AGCTCTATCATTGGTGGTCATCATCAGCAATTTATTGAGAAAGGTTTATTGTCACATTTA
AAATTGCTCCCAGAATTTGAGAATGATGAAAGAATAGTTGGAATAATAAAAGGTTTACAT
ACATCGTATGTTGGTAAAGATTATACAGTGAACAAAGATGCTGATGTTCCTATTGAAAGC
TTAGATCAACTTTCACTCAAGTCTTATCCACTTTGTATGCGAATGTGTCATGAATCGTTA
AGAAAAACTCATCATTTAAAGCATTCTGGTCGTTTGCAGTATGGTCTGTTTTTAAAAGGA
ATTGGTGTTTCATTGGAAGATTCACTCCGATTTTGGCGTGAAGAAATGACTAAGAATATG
GAAGTAGATAAATTTGATAAAAGTTATGCATATGGTATTCGATATAATTATGGAAAGGAA
GGATCAAGAACAAACTGGACTCCTTGGTCATGTGCCAAAATTATTTCAACCGCTCCAGGT
GCTCAAGACGTTGCTGGTTGTCCATTTAAATTATGGGATTCAATTGAGCTAAAATCAAAA
TTAACAAGTTTTGGTCTCAATCCTATGGCAGTTCAGGATGTTGTGAGTTATGCTAGTAAA
GGACATTTTCAATTAGCTTGTGGACGTTATTTCGAGTCAGTACATGAAACTAGACTTGAT
GAAGGTGTTAATCATCCAAATGGTTACTTTGAAAATAGTCAAATAATAATGGGCAACAGG
CAGACAAAAGAAAAGAATAAACCTTCTTCACAACAGTCCAATTTTAATCATCGTAAGCAA
GTTCAGATGAACAAACAACAAGAATTCAAACGTAAAATGGACATAAAAATTAAAGAAGAA
AAAGATTTTGATGAAGAGCTGTGGAAATTATCACAACGTGAGGAGGAATTATTGAATGAA
TGGAATACACGACAAGAGCAAACTAAAAAAGAAGTTGCTGAAATTTCTCAAATGGATTGG
AATGATGATGATGAAGACATGTCTCAAATTAATAATTATTTGTAA
>g12532.t1 Gene=g12532 Length=554
MDFTKRSRIKLLKSPDEDSIDRFAPHNCMFYILPPQNDVSLKDFEDLAIERLKLLRILEQ
ASLKYPKILSDEWKEFIINELNAEGLKYFVRLIKGNGNSEQDKHARRRDYLSHFILRFAY
CRSEELRRWFITREMELFKFKFSSLSSNEIKDFIELYEMGYRPITDEQKNEVRQELQCSS
TGNIDTIDFYKVNFLQVLDLVRQRKCFLKGGFAYVSSNDFSSIIGGHHQQFIEKGLLSHL
KLLPEFENDERIVGIIKGLHTSYVGKDYTVNKDADVPIESLDQLSLKSYPLCMRMCHESL
RKTHHLKHSGRLQYGLFLKGIGVSLEDSLRFWREEMTKNMEVDKFDKSYAYGIRYNYGKE
GSRTNWTPWSCAKIISTAPGAQDVAGCPFKLWDSIELKSKLTSFGLNPMAVQDVVSYASK
GHFQLACGRYFESVHETRLDEGVNHPNGYFENSQIIMGNRQTKEKNKPSSQQSNFNHRKQ
VQMNKQQEFKRKMDIKIKEEKDFDEELWKLSQREEELLNEWNTRQEQTKKEVAEISQMDW
NDDDEDMSQINNYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12532.t1 | CDD | cd07322 | PriL_PriS_Eukaryotic | 30 | 453 | 5.32404E-171 |
| 7 | g12532.t1 | Coils | Coil | Coil | 511 | 531 | - |
| 6 | g12532.t1 | Gene3D | G3DSA:1.20.930.80 | - | 4 | 259 | 9.5E-73 |
| 4 | g12532.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 461 | 482 | - |
| 5 | g12532.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 461 | 487 | - |
| 2 | g12532.t1 | PANTHER | PTHR10537 | DNA PRIMASE LARGE SUBUNIT | 25 | 488 | 9.9E-143 |
| 3 | g12532.t1 | PANTHER | PTHR10537:SF3 | DNA PRIMASE LARGE SUBUNIT | 25 | 488 | 9.9E-143 |
| 8 | g12532.t1 | PIRSF | PIRSF009449 | DNA_primase_large | 3 | 483 | 3.1E-159 |
| 1 | g12532.t1 | Pfam | PF04104 | Eukaryotic and archaeal DNA primase, large subunit | 188 | 450 | 1.0E-76 |
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 transcript has been annotated with K02685 (DNA primase large subunit)
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.
