Gene loci information

Transcript annotation

  • This transcript has been annotated as Replication protein A 70 kDa DNA-binding subunit.

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 g657 g657.t4 TTS g657.t4 5028704 5028704
chr_3 g657 g657.t4 isoform g657.t4 5028969 5030707
chr_3 g657 g657.t4 exon g657.t4.exon1 5028969 5030397
chr_3 g657 g657.t4 cds g657.t4.CDS1 5028969 5030397
chr_3 g657 g657.t4 exon g657.t4.exon2 5030454 5030707
chr_3 g657 g657.t4 cds g657.t4.CDS2 5030454 5030569
chr_3 g657 g657.t4 TSS g657.t4 5030951 5030951

Sequences

>g657.t4 Gene=g657 Length=1683
AGAATCGTTCAAGGAGAAGATTGCCCTTGTCCTCTTGTCTTTCAAGTAATTGGTTCAAAG
AGAGTGCAATCAACTTCAGATGCACCAGATCGTTGTCGCTTAGTTTTGAATGATGGTGTA
ACTCAACATGGATTTGCAATGTTATCTGCAAATTTAAATGGAAGATACGCTAATGGAGAG
TTTGATGATTACTCAATCATTCGTATCGATCGTTTTGTACCTTCACGAGTTAATCGCAAT
AATCCGAATGATAAAAATGTCATCATTTTGTTTGATATCGAGACTTTACACAGTGGAAAA
GAAGTTGGTGAACCCATTTCTGCAAATTCTGAATCACTTTCATCATCATCATCATCAAAT
TCTGTTCCTGCACCTCAAAAAGAAAATGTCAATACAAATACAAATTCACGATATTCAACA
TCTGCAAATAACCCAAATACATCTTTAAATCTTAATTCAAGTATGGCAGGTGATTTGAGT
GAACATCTCACAATGCCAATCGATTCATTGAGTCCTTATCAAAATAAGTGGGTAATTAAG
GCTCGTGTTACAGCAAAGTCATCAATTCGTTCTTGGAAGAATGAAAAAGGCGAAGGAAAA
CTCTTTAACGTTGATCTTTGTGATGAATCTGGTGAAATTCGATGCACTGGTTTTCGTGAT
TCAGTTGATCGTTTCTATGATTTACTTGAAATTGGCAAGGTTTATTATATTAGCAAATGC
CAGTTGAAACCAGCAAACAAGAAATATTCAAAAATCAACAATGATTATGAGATGACAATG
TCTAGTGAAACTCAAATTCAGCCTTGTTCTGATGACACATCGAGTATTCCAAAAATCAAA
TATAATCTTGTTTCGATTTCTGATTTGGCAGGAAAACCTAAGGATGACATTGTTGATGTA
ATTGGTATTGCTCGTGAAATAGGACAAGTCACTAATATTGTTGCACGGGCATCTGGGCAG
CAACTAACTAAACGAGAAGTCACCATTGCTGATCAAACAAACGCATCAATTGTTCTTACC
TTATGGGGCGCTGAGGCCGAAAATTTTTCTGGTTTTGATAATCCTGTAGTTTTAGCTAAG
AATGTAAGAATTGGCGAATATGGTGGTGGTAAAACATTGGGAACAACTGTAAGCTCAACT
GTTTTAGTAAATCCTGAGATGCCTGAAGCACATCAATTGAAAGGCTGGTATGATAACAAT
GCTTCAAAATGTTCATTCGTTGGTTTATCACAACGCACAGCAGGTCCAAGCTCAGCTTAT
CAATGGGCTACTTTCAATGATTGCTTGAAGAAACAATTTGGTATTGATAAGGCTGATTAT
TTCCAAACAATGGCGATGATTCACATGATTCGTATTGAAAACATGTTCTACAAAGCTTGC
CCAAGTGAAAGTTGCAACAAGAAAGTAATTGATTCTGGAAATGGCGTGTATCGATGTGAG
AAATGTAACGCTGAATCGCCAAATTATTCTAATCGTATGCTGGCTAATGTATTACTTGGT
GACTCAACTTCAAATCGTTGGGTTACTCTTTTTGCTAATGTCGGAGAAAAACTTTTTGGC
AAGAATACTGATGAATTGGTAAGAATCAAAGAAAATGATAAGAATGAGTTTGACAATTTG
ATACAAAAGATACTCTTCAAACCTCAAATTTATAAATTGCGTACCCAAACTGAGACATAC
AAT

>g657.t4 Gene=g657 Length=515
MLSANLNGRYANGEFDDYSIIRIDRFVPSRVNRNNPNDKNVIILFDIETLHSGKEVGEPI
SANSESLSSSSSSNSVPAPQKENVNTNTNSRYSTSANNPNTSLNLNSSMAGDLSEHLTMP
IDSLSPYQNKWVIKARVTAKSSIRSWKNEKGEGKLFNVDLCDESGEIRCTGFRDSVDRFY
DLLEIGKVYYISKCQLKPANKKYSKINNDYEMTMSSETQIQPCSDDTSSIPKIKYNLVSI
SDLAGKPKDDIVDVIGIAREIGQVTNIVARASGQQLTKREVTIADQTNASIVLTLWGAEA
ENFSGFDNPVVLAKNVRIGEYGGGKTLGTTVSSTVLVNPEMPEAHQLKGWYDNNASKCSF
VGLSQRTAGPSSAYQWATFNDCLKKQFGIDKADYFQTMAMIHMIRIENMFYKACPSESCN
KKVIDSGNGVYRCEKCNAESPNYSNRMLANVLLGDSTSNRWVTLFANVGEKLFGKNTDEL
VRIKENDKNEFDNLIQKILFKPQIYKLRTQTETYN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g657.t4 CDD cd04474 RPA1_DBD_A 120 222 7.31235E-52
15 g657.t4 CDD cd04475 RPA1_DBD_B 251 352 1.01153E-37
16 g657.t4 CDD cd04476 RPA1_DBD_C 390 515 1.30292E-43
10 g657.t4 Gene3D G3DSA:2.40.50.140 - 1 65 2.7E-7
13 g657.t4 Gene3D G3DSA:2.40.50.140 - 118 226 2.1E-42
11 g657.t4 Gene3D G3DSA:2.40.50.140 - 228 362 4.1E-39
12 g657.t4 Gene3D G3DSA:2.40.50.140 - 363 515 2.7E-42
9 g657.t4 MobiDBLite mobidb-lite consensus disorder prediction 61 101 -
4 g657.t4 PANTHER PTHR23273 REPLICATION FACTOR A 1, RFA1 1 515 1.1E-89
5 g657.t4 PANTHER PTHR23273:SF47 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT A 1 515 1.1E-89
1 g657.t4 Pfam PF01336 OB-fold nucleic acid binding domain 131 211 3.6E-13
2 g657.t4 Pfam PF16900 Replication protein A OB domain 240 338 7.5E-26
3 g657.t4 Pfam PF08646 Replication factor-A C terminal domain 394 515 8.1E-39
8 g657.t4 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 119 229 2.69E-32
7 g657.t4 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 235 355 2.86E-30
6 g657.t4 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 374 515 1.71E-41
14 g657.t4 TIGRFAM TIGR00617 rpa1: replication factor-a protein 1 (rpa1) 1 515 7.5E-166

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:0005634 nucleus CC
GO:0003677 DNA binding MF
GO:0006281 DNA repair BP
GO:0006260 DNA replication BP
GO:0006310 DNA recombination BP
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