General information for g2623.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Single-stranded DNA-binding protein, mitochondrial.
Parent gene
- The parent gene g2623 is located on chr_3: 19155167..19158970 (- 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 | g2623 | g2623.t1 | TTS | g2623.t1 | 19154862 | 19154862 |
| chr_3 | g2623 | g2623.t1 | isoform | g2623.t1 | 19154977 | 19155570 |
| chr_3 | g2623 | g2623.t1 | exon | g2623.t1.exon1 | 19154977 | 19155190 |
| chr_3 | g2623 | g2623.t1 | cds | g2623.t1.CDS1 | 19154977 | 19155190 |
| chr_3 | g2623 | g2623.t1 | exon | g2623.t1.exon2 | 19155258 | 19155366 |
| chr_3 | g2623 | g2623.t1 | cds | g2623.t1.CDS2 | 19155258 | 19155366 |
| chr_3 | g2623 | g2623.t1 | exon | g2623.t1.exon3 | 19155429 | 19155492 |
| chr_3 | g2623 | g2623.t1 | cds | g2623.t1.CDS3 | 19155429 | 19155492 |
| chr_3 | g2623 | g2623.t1 | exon | g2623.t1.exon4 | 19155562 | 19155570 |
| chr_3 | g2623 | g2623.t1 | cds | g2623.t1.CDS4 | 19155562 | 19155570 |
| chr_3 | g2623 | g2623.t1 | TSS | g2623.t1 | 19155590 | 19155590 |
Sequences
>g2623.t1 Gene=g2623 Length=396
ATGAATCGATTATTTGCAAGAGCCATTAGTTCAAGATTATTTTCAAGTGATAGTCCAACA
CGTATTGAAAAGACAATCAATACTGTCACTTTGCTTGGAAGAGTAGGAGCAGATCCACAG
AAACGAGGAAATGATCAACATCCATGCGTTACTTTCTCTGTAGCAACTCACAATAATTAT
AAGTATGAAAGTGGTGATTGGATACAGAAAACTGATTGGCACAGAGTTGTAATATTCAAA
CCTCAATTAAGCGATTCAGTTTATCAATATATGAAGAAAGGACAACGCTGTTTAGTTACC
GGAAAAATTTCTTATGGAGAAATCACAGATCAAGAAGGAAAAACTAGAATGAGCACAAGC
ATCATTGCAGATGAAGTAGTCTTTTTTCAAACTTAA
>g2623.t1 Gene=g2623 Length=131
MNRLFARAISSRLFSSDSPTRIEKTINTVTLLGRVGADPQKRGNDQHPCVTFSVATHNNY
KYESGDWIQKTDWHRVVIFKPQLSDSVYQYMKKGQRCLVTGKISYGEITDQEGKTRMSTS
IIADEVVFFQT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2623.t1 | CDD | cd04496 | SSB_OBF | 29 | 128 | 0.00000 |
| 6 | g2623.t1 | Gene3D | G3DSA:2.40.50.140 | - | 15 | 131 | 0.00000 |
| 4 | g2623.t1 | Hamap | MF_00984 | Single-stranded DNA-binding protein. | 26 | 130 | 24.61956 |
| 2 | g2623.t1 | PANTHER | PTHR10302 | SINGLE-STRANDED DNA-BINDING PROTEIN | 12 | 128 | 0.00000 |
| 3 | g2623.t1 | PANTHER | PTHR10302:SF0 | SINGLE-STRANDED DNA-BINDING PROTEIN, MITOCHONDRIAL | 12 | 128 | 0.00000 |
| 7 | g2623.t1 | PIRSF | PIRSF002070 | SSB | 22 | 131 | 0.00000 |
| 1 | g2623.t1 | Pfam | PF00436 | Single-strand binding protein family | 26 | 128 | 0.00000 |
| 10 | g2623.t1 | ProSiteProfiles | PS50935 | Single-strand binding (SSB) domain profile. | 26 | 130 | 24.54400 |
| 5 | g2623.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 26 | 129 | 0.00000 |
| 9 | g2623.t1 | TIGRFAM | TIGR00621 | ssb: single-stranded DNA-binding protein | 23 | 129 | 0.00000 |
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:0003697 | single-stranded DNA binding | MF |
| GO:0006260 | DNA replication | BP |
KEGG
Orthology
- This transcript has been annotated with K03111 (single-strand DNA-binding protein)
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.
