Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Replication protein A 32 kDa subunit-A.

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 g2169 g2169.t1 TTS g2169.t1 15774749 15774749
chr_3 g2169 g2169.t1 isoform g2169.t1 15775089 15776043
chr_3 g2169 g2169.t1 exon g2169.t1.exon1 15775089 15775606
chr_3 g2169 g2169.t1 cds g2169.t1.CDS1 15775089 15775606
chr_3 g2169 g2169.t1 exon g2169.t1.exon2 15775667 15775826
chr_3 g2169 g2169.t1 cds g2169.t1.CDS2 15775667 15775826
chr_3 g2169 g2169.t1 exon g2169.t1.exon3 15775883 15775938
chr_3 g2169 g2169.t1 cds g2169.t1.CDS3 15775883 15775938
chr_3 g2169 g2169.t1 exon g2169.t1.exon4 15776031 15776043
chr_3 g2169 g2169.t1 cds g2169.t1.CDS4 15776031 15776043
chr_3 g2169 g2169.t1 TSS g2169.t1 15776187 15776187

Sequences

>g2169.t1 Gene=g2169 Length=747
ATGAACGATAGTTTTGGAGGAGGATTTACTCAATCAGCTACTGATTCAAAGACGGAATCA
AAGACTGAGGGAACGTTGCCAGTTTTCATAAAAATGATTCTTTTGCAAAATGATATTGAA
GCAGTTTCATTGTTTGGTCAAGATCATAAGATGGTCAATTTAGTTGCAGTTGTCAAAAAT
ATTGAACATTCGTCAACAAAAATCTCATATGAACTCGAAGATTTTACAGGACGCATAACT
GCCAATTTATGGATCGATGAAGATGTTCCTCGTAATCAAAATATCATGATTAACAGTTAT
GTACGAGTCATAGGAGGTGTGAGATGTCAAAATAGTGCAAAATCAATTATGGTTTATAAA
ATTGATCCTGTTGGTGGTATCAATGAAATAAATACGCATTATATTGAAGTTGTCAATGCA
CGTTATGCAGCTGAAGAAAATGCAGGCGGCTCAACTTCTAATGATTCTAAAATGGATGTC
GATGTTCATGTTCCAAATAAGAGTGCTGGTGGTGATGCTGGAATAGCTGATAGTGATTTG
GAAGGTCTTAATGCTAAAGAGAGAGTGGTTTTCAAAATGATTCAAGGTGCATTAGAAACT
ACAGTTGAAGGATATCATCGAAGTGAAGTTTACAAACGTTTTCCACAATTTTCAAAAGAT
GAAATCGATACTATGCTTGAACGAATGTCGACAGAAGGCTTGATTTATACCACTGTTGAT
ACGGATCATTTCCAAGCTTGTTTCTAA

>g2169.t1 Gene=g2169 Length=248
MNDSFGGGFTQSATDSKTESKTEGTLPVFIKMILLQNDIEAVSLFGQDHKMVNLVAVVKN
IEHSSTKISYELEDFTGRITANLWIDEDVPRNQNIMINSYVRVIGGVRCQNSAKSIMVYK
IDPVGGINEINTHYIEVVNARYAAEENAGGSTSNDSKMDVDVHVPNKSAGGDAGIADSDL
EGLNAKERVVFKMIQGALETTVEGYHRSEVYKRFPQFSKDEIDTMLERMSTEGLIYTTVD
TDHFQACF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2169.t1 CDD cd04478 RPA2_DBD_D 51 142 4.05183E-27
8 g2169.t1 Gene3D G3DSA:2.40.50.140 - 18 144 6.6E-27
9 g2169.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 177 248 1.6E-15
7 g2169.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
3 g2169.t1 PANTHER PTHR13989:SF16 REPLICATION PROTEIN A2 6 247 1.3E-28
4 g2169.t1 PANTHER PTHR13989 REPLICATION PROTEIN A-RELATED 6 247 1.3E-28
1 g2169.t1 Pfam PF01336 OB-fold nucleic acid binding domain 52 122 1.5E-6
2 g2169.t1 Pfam PF08784 Replication protein A C terminal 150 241 4.9E-7
6 g2169.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 27 142 1.51E-19
5 g2169.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 182 246 7.07E-9

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:0003676 nucleic acid binding MF

KEGG

Orthology

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.

Raw TPM values