Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Single-stranded DNA-binding protein, mitochondrial.

Parent gene

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.t2 TTS g2623.t2 19154862 19154862
chr_3 g2623 g2623.t2 isoform g2623.t2 19154977 19155570
chr_3 g2623 g2623.t2 exon g2623.t2.exon1 19154977 19155190
chr_3 g2623 g2623.t2 cds g2623.t2.CDS1 19154977 19155190
chr_3 g2623 g2623.t2 exon g2623.t2.exon2 19155258 19155570
chr_3 g2623 g2623.t2 cds g2623.t2.CDS2 19155258 19155388
chr_3 g2623 g2623.t2 TSS g2623.t2 19155590 19155590

Sequences

>g2623.t2 Gene=g2623 Length=527
ATGAATCGAGTAAGATTTTTAAGTTTATTATATTCGAGTGATTTCTCAATGATTTTAATA
TCTTTATTCATGTTTTAGTTATTTGCAAGAGCCATTAGTTCAAGATTATTTTCAAGTGAT
AGTCCAACACGTATTGAAAAGAGTAAGAAATTTTGTTTAAAATAACCTACCATAATTTCA
TAATGTTTTTGTTCATTTCTTTAGCAATCAATACTGTCACTTTGCTTGGAAGAGTAGGAG
CAGATCCACAGAAACGAGGAAATGATCAACATCCATGCGTTACTTTCTCTGTAGCAACTC
ACAATAATTATAAGTATGAAAGTGGTGATTGGATACAGAAAACTGATTGGCACAGAGTTG
TAATATTCAAACCTCAATTAAGCGATTCAGTTTATCAATATATGAAGAAAGGACAACGCT
GTTTAGTTACCGGAAAAATTTCTTATGGAGAAATCACAGATCAAGAAGGAAAAACTAGAA
TGAGCACAAGCATCATTGCAGATGAAGTAGTCTTTTTTCAAACTTAA

>g2623.t2 Gene=g2623 Length=114
MFLFISLAINTVTLLGRVGADPQKRGNDQHPCVTFSVATHNNYKYESGDWIQKTDWHRVV
IFKPQLSDSVYQYMKKGQRCLVTGKISYGEITDQEGKTRMSTSIIADEVVFFQT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g2623.t2 CDD cd04496 SSB_OBF 12 111 1.4768E-28
8 g2623.t2 Gene3D G3DSA:2.40.50.140 - 3 114 5.4E-33
4 g2623.t2 Hamap MF_00984 Single-stranded DNA-binding protein. 9 113 24.619556
2 g2623.t2 PANTHER PTHR10302 SINGLE-STRANDED DNA-BINDING PROTEIN 9 111 1.0E-22
3 g2623.t2 PANTHER PTHR10302:SF0 SINGLE-STRANDED DNA-BINDING PROTEIN, MITOCHONDRIAL 9 111 1.0E-22
14 g2623.t2 PIRSF PIRSF002070 SSB 5 114 1.4E-37
1 g2623.t2 Pfam PF00436 Single-strand binding protein family 9 111 3.7E-28
10 g2623.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
11 g2623.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
12 g2623.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 15 -
13 g2623.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 16 20 -
9 g2623.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 114 -
17 g2623.t2 ProSiteProfiles PS50935 Single-strand binding (SSB) domain profile. 9 113 24.544
5 g2623.t2 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 9 112 1.65E-27
7 g2623.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
6 g2623.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 20 -
16 g2623.t2 TIGRFAM TIGR00621 ssb: single-stranded DNA-binding protein 8 112 1.3E-28

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 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.

Raw TPM values