General information for g657.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Replication protein A 70 kDa DNA-binding subunit.
Parent gene
- The parent gene g657 is located on chr_3: 5030465..5030818 (- 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_3 | g657 | g657.t2 | TTS | g657.t2 | 5028704 | 5028704 |
| chr_3 | g657 | g657.t2 | isoform | g657.t2 | 5028786 | 5029552 |
| chr_3 | g657 | g657.t2 | exon | g657.t2.exon1 | 5028786 | 5028902 |
| chr_3 | g657 | g657.t2 | cds | g657.t2.CDS1 | 5028786 | 5028902 |
| chr_3 | g657 | g657.t2 | exon | g657.t2.exon2 | 5028969 | 5029552 |
| chr_3 | g657 | g657.t2 | cds | g657.t2.CDS2 | 5028969 | 5029493 |
| chr_3 | g657 | g657.t2 | TSS | g657.t2 | NA | NA |
Sequences
>g657.t2 Gene=g657 Length=701
ATGGTGGTGGTAAAACATTGGGAACAACTGTAAGCTCAACTGTTTTAGTAAATCCTGAGA
TGCCTGAAGCACATCAATTGAAAGGCTGGTATGATAACAATGCTTCAAAATGTTCATTCG
TTGGTTTATCACAACGCACAGCAGGTCCAAGCTCAGCTTATCAATGGGCTACTTTCAATG
ATTGCTTGAAGAAACAATTTGGTATTGATAAGGCTGATTATTTCCAAACAATGGCGATGA
TTCACATGATTCGTATTGAAAACATGTTCTACAAAGCTTGCCCAAGTGAAAGTTGCAACA
AGAAAGTAATTGATTCTGGAAATGGCGTGTATCGATGTGAGAAATGTAACGCTGAATCGC
CAAATTATTCTAATCGTATGCTGGCTAATGTATTACTTGGTGACTCAACTTCAAATCGTT
GGGTTACTCTTTTTGCTAATGTCGGAGAAAAACTTTTTGGCAAGAATACTGATGAATTGG
TAAGAATCAAAGAAAATGATAAGAATGAGTTTGACAATTTGATACAAAAGATACTCTTCA
AACCTCAAATTTATAAATTGCGTACCCAAACTGAGACATACAATGATGTACCACGAAACA
AGATCACTTGTGTTGCTGTTGGAGAAACAAAAATTAAAGATTATAATCAGCATTTGCTTG
CAAACATTCAACGTTTGACTGGAATCTGCGTTGATAAATAA
>g657.t2 Gene=g657 Length=213
MPEAHQLKGWYDNNASKCSFVGLSQRTAGPSSAYQWATFNDCLKKQFGIDKADYFQTMAM
IHMIRIENMFYKACPSESCNKKVIDSGNGVYRCEKCNAESPNYSNRMLANVLLGDSTSNR
WVTLFANVGEKLFGKNTDELVRIKENDKNEFDNLIQKILFKPQIYKLRTQTETYNDVPRN
KITCVAVGETKIKDYNQHLLANIQRLTGICVDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g657.t2 | CDD | cd04476 | RPA1_DBD_C | 50 | 203 | 0 |
| 5 | g657.t2 | Gene3D | G3DSA:2.40.50.140 | - | 21 | 206 | 0 |
| 2 | g657.t2 | PANTHER | PTHR23273 | REPLICATION FACTOR A 1, RFA1 | 1 | 202 | 0 |
| 3 | g657.t2 | PANTHER | PTHR23273:SF47 | REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT A | 1 | 202 | 0 |
| 1 | g657.t2 | Pfam | PF08646 | Replication factor-A C terminal domain | 54 | 199 | 0 |
| 4 | g657.t2 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 34 | 206 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
