General information for g13888.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA primase small subunit.
Parent gene
- The parent gene g13888 is located on chr_1: 33112813..33114160 (- 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 | g13888 | g13888.t2 | TTS | g13888.t2 | 33112761 | 33112761 |
| chr_1 | g13888 | g13888.t2 | isoform | g13888.t2 | 33112813 | 33113974 |
| chr_1 | g13888 | g13888.t2 | exon | g13888.t2.exon1 | 33112813 | 33113974 |
| chr_1 | g13888 | g13888.t2 | cds | g13888.t2.CDS1 | 33112813 | 33113931 |
| chr_1 | g13888 | g13888.t2 | TSS | g13888.t2 | 33114220 | 33114220 |
Sequences
>g13888.t2 Gene=g13888 Length=1162
AGCTGAAGATGGAATATTTACGAATAGAGAATTCTCATTTACAATGGAGGATGACATTTA
TATACGATATTTATCATTCGAAAATCAATCAGAATTGGAAAATGATATTTGTACAAAAAT
ACCACATAAAATCGATATTGGTGCAGTTTTTAATACGAGGCCAAAAAATCATCGTTCAAA
TGCAAACATGAAGCCTATTCAAAGAGAATTGGTTTTTGATATCGATATGACTGATTACGA
TGATGTTAGAACGTGTTGCAATGAAGCAAATATTTGCAATAAATGTTGGAAATTTATGTC
CATTGCATGCAAAGTAATCGATACAGCACTGCGTGAGGATTTCGGCTTTGAACATCTACT
GTGGGTTTTCTCAGGACGTCGTGGTATTCATTGTTGGGTATGCGATAAAACAGCACGTCA
TCTCGATAGTAAAGGAAGAGGAGCTATTGCAGATTATTTACAAGTCTCAATGAGTGGAGG
AGGAGAAAATACTGTCACTAAAGTAACATTATATGACAAGCAACATCACAGTATTCGTCG
TGCACGTACAATCATCGAACCATGTTTCAATGAAATCATAATTGAGGATCAAGACGCATT
CGGCTCACCAAGTGGCATTGATAAATTACTGAAAATGGTAAATGACGAGACATGTAGAAA
AGAACTACAAAATTTATTCGCTTCAACAGCGTCAGACTCAAAAAGCATCTGGAGTACTTT
TGTTGGATATTTCGAATCGATGCGAGTAAAGAGCCAATTAAAGTCAAAACTAAAATATAT
TGTTGAAGAAGTGCAACTGGCTATGCTATATCCACGTCTCGATATCAACGTCAGTCGTGG
CACTAATCACTTGTTAAAAGCACCATTCTGTGTGCATCCTAAAACTGGAAAAGTCTGCGT
GCCTTTTAATCCAAATCTTGCTCATAAATTTGATCCAATGACTGTCCCTACAGTCAACTT
GTTAATGAAAGAAATTGATGAATTCGACCAAAAGACCAATGAAGCATTAGAAACACCAGA
TGATAAAGCAGCTAAAGTGAAGGATTTCAAGAAAACTTCAATGTTTAAATCAACAGTAAT
TTTTGAAGAGTTTTTGAGAAAAATTGAACAGAGCACAAAATCTAAAGCAATTACTGTGAG
TGATAAACGAATGGAATTTTGA
>g13888.t2 Gene=g13888 Length=372
MEDDIYIRYLSFENQSELENDICTKIPHKIDIGAVFNTRPKNHRSNANMKPIQRELVFDI
DMTDYDDVRTCCNEANICNKCWKFMSIACKVIDTALREDFGFEHLLWVFSGRRGIHCWVC
DKTARHLDSKGRGAIADYLQVSMSGGGENTVTKVTLYDKQHHSIRRARTIIEPCFNEIII
EDQDAFGSPSGIDKLLKMVNDETCRKELQNLFASTASDSKSIWSTFVGYFESMRVKSQLK
SKLKYIVEEVQLAMLYPRLDINVSRGTNHLLKAPFCVHPKTGKVCVPFNPNLAHKFDPMT
VPTVNLLMKEIDEFDQKTNEALETPDDKAAKVKDFKKTSMFKSTVIFEEFLRKIEQSTKS
KAITVSDKRMEF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13888.t2 | CDD | cd04860 | AE_Prim_S | 1 | 298 | 0 |
| 5 | g13888.t2 | Gene3D | G3DSA:3.90.920.30 | - | 1 | 360 | 0 |
| 2 | g13888.t2 | PANTHER | PTHR10536 | DNA PRIMASE SMALL SUBUNIT | 2 | 372 | 0 |
| 3 | g13888.t2 | PANTHER | PTHR10536:SF0 | DNA PRIMASE SMALL SUBUNIT | 2 | 372 | 0 |
| 1 | g13888.t2 | Pfam | PF01896 | DNA primase small subunit | 58 | 289 | 0 |
| 4 | g13888.t2 | SUPERFAMILY | SSF56747 | Prim-pol domain | 2 | 319 | 0 |
| 6 | g13888.t2 | TIGRFAM | TIGR00335 | primase_sml: putative DNA primase, eukaryotic-type, small subunit | 5 | 305 | 0 |
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 |
| GO:0003896 | DNA primase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K02684 (DNA primase small 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.
