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.t5 TTS g657.t5 5028704 5028704
chr_3 g657 g657.t5 isoform g657.t5 5028969 5030818
chr_3 g657 g657.t5 exon g657.t5.exon1 5028969 5030397
chr_3 g657 g657.t5 cds g657.t5.CDS1 5028969 5030397
chr_3 g657 g657.t5 exon g657.t5.exon2 5030454 5030707
chr_3 g657 g657.t5 cds g657.t5.CDS2 5030454 5030707
chr_3 g657 g657.t5 exon g657.t5.exon3 5030777 5030818
chr_3 g657 g657.t5 cds g657.t5.CDS3 5030777 5030818
chr_3 g657 g657.t5 TSS g657.t5 5030951 5030951

Sequences

>g657.t5 Gene=g657 Length=1725
ATGGCAAAATATTTGACGAAGTTGTCAGTTGGAAAATTGGCTAGAATCGTTCAAGGAGAA
GATTGCCCTTGTCCTCTTGTCTTTCAAGTAATTGGTTCAAAGAGAGTGCAATCAACTTCA
GATGCACCAGATCGTTGTCGCTTAGTTTTGAATGATGGTGTAACTCAACATGGATTTGCA
ATGTTATCTGCAAATTTAAATGGAAGATACGCTAATGGAGAGTTTGATGATTACTCAATC
ATTCGTATCGATCGTTTTGTACCTTCACGAGTTAATCGCAATAATCCGAATGATAAAAAT
GTCATCATTTTGTTTGATATCGAGACTTTACACAGTGGAAAAGAAGTTGGTGAACCCATT
TCTGCAAATTCTGAATCACTTTCATCATCATCATCATCAAATTCTGTTCCTGCACCTCAA
AAAGAAAATGTCAATACAAATACAAATTCACGATATTCAACATCTGCAAATAACCCAAAT
ACATCTTTAAATCTTAATTCAAGTATGGCAGGTGATTTGAGTGAACATCTCACAATGCCA
ATCGATTCATTGAGTCCTTATCAAAATAAGTGGGTAATTAAGGCTCGTGTTACAGCAAAG
TCATCAATTCGTTCTTGGAAGAATGAAAAAGGCGAAGGAAAACTCTTTAACGTTGATCTT
TGTGATGAATCTGGTGAAATTCGATGCACTGGTTTTCGTGATTCAGTTGATCGTTTCTAT
GATTTACTTGAAATTGGCAAGGTTTATTATATTAGCAAATGCCAGTTGAAACCAGCAAAC
AAGAAATATTCAAAAATCAACAATGATTATGAGATGACAATGTCTAGTGAAACTCAAATT
CAGCCTTGTTCTGATGACACATCGAGTATTCCAAAAATCAAATATAATCTTGTTTCGATT
TCTGATTTGGCAGGAAAACCTAAGGATGACATTGTTGATGTAATTGGTATTGCTCGTGAA
ATAGGACAAGTCACTAATATTGTTGCACGGGCATCTGGGCAGCAACTAACTAAACGAGAA
GTCACCATTGCTGATCAAACAAACGCATCAATTGTTCTTACCTTATGGGGCGCTGAGGCC
GAAAATTTTTCTGGTTTTGATAATCCTGTAGTTTTAGCTAAGAATGTAAGAATTGGCGAA
TATGGTGGTGGTAAAACATTGGGAACAACTGTAAGCTCAACTGTTTTAGTAAATCCTGAG
ATGCCTGAAGCACATCAATTGAAAGGCTGGTATGATAACAATGCTTCAAAATGTTCATTC
GTTGGTTTATCACAACGCACAGCAGGTCCAAGCTCAGCTTATCAATGGGCTACTTTCAAT
GATTGCTTGAAGAAACAATTTGGTATTGATAAGGCTGATTATTTCCAAACAATGGCGATG
ATTCACATGATTCGTATTGAAAACATGTTCTACAAAGCTTGCCCAAGTGAAAGTTGCAAC
AAGAAAGTAATTGATTCTGGAAATGGCGTGTATCGATGTGAGAAATGTAACGCTGAATCG
CCAAATTATTCTAATCGTATGCTGGCTAATGTATTACTTGGTGACTCAACTTCAAATCGT
TGGGTTACTCTTTTTGCTAATGTCGGAGAAAAACTTTTTGGCAAGAATACTGATGAATTG
GTAAGAATCAAAGAAAATGATAAGAATGAGTTTGACAATTTGATACAAAAGATACTCTTC
AAACCTCAAATTTATAAATTGCGTACCCAAACTGAGACATACAAT

>g657.t5 Gene=g657 Length=575
MAKYLTKLSVGKLARIVQGEDCPCPLVFQVIGSKRVQSTSDAPDRCRLVLNDGVTQHGFA
MLSANLNGRYANGEFDDYSIIRIDRFVPSRVNRNNPNDKNVIILFDIETLHSGKEVGEPI
SANSESLSSSSSSNSVPAPQKENVNTNTNSRYSTSANNPNTSLNLNSSMAGDLSEHLTMP
IDSLSPYQNKWVIKARVTAKSSIRSWKNEKGEGKLFNVDLCDESGEIRCTGFRDSVDRFY
DLLEIGKVYYISKCQLKPANKKYSKINNDYEMTMSSETQIQPCSDDTSSIPKIKYNLVSI
SDLAGKPKDDIVDVIGIAREIGQVTNIVARASGQQLTKREVTIADQTNASIVLTLWGAEA
ENFSGFDNPVVLAKNVRIGEYGGGKTLGTTVSSTVLVNPEMPEAHQLKGWYDNNASKCSF
VGLSQRTAGPSSAYQWATFNDCLKKQFGIDKADYFQTMAMIHMIRIENMFYKACPSESCN
KKVIDSGNGVYRCEKCNAESPNYSNRMLANVLLGDSTSNRWVTLFANVGEKLFGKNTDEL
VRIKENDKNEFDNLIQKILFKPQIYKLRTQTETYN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g657.t5 CDD cd04474 RPA1_DBD_A 180 282 2.66535E-52
17 g657.t5 CDD cd04475 RPA1_DBD_B 311 412 1.12459E-37
18 g657.t5 CDD cd04476 RPA1_DBD_C 450 575 1.86787E-43
12 g657.t5 Gene3D G3DSA:2.40.50.140 - 6 125 9.3E-22
13 g657.t5 Gene3D G3DSA:2.40.50.140 - 178 286 2.5E-42
14 g657.t5 Gene3D G3DSA:2.40.50.140 - 288 422 5.0E-39
15 g657.t5 Gene3D G3DSA:2.40.50.140 - 423 575 3.3E-42
11 g657.t5 MobiDBLite mobidb-lite consensus disorder prediction 121 161 -
5 g657.t5 PANTHER PTHR23273 REPLICATION FACTOR A 1, RFA1 7 575 1.7E-94
6 g657.t5 PANTHER PTHR23273:SF47 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT A 7 575 1.7E-94
3 g657.t5 Pfam PF04057 Replication factor-A protein 1, N-terminal domain 8 111 8.0E-14
1 g657.t5 Pfam PF01336 OB-fold nucleic acid binding domain 191 271 4.2E-13
2 g657.t5 Pfam PF16900 Replication protein A OB domain 300 398 9.0E-26
4 g657.t5 Pfam PF08646 Replication factor-A C terminal domain 454 575 9.8E-39
10 g657.t5 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 7 120 2.23E-16
8 g657.t5 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 179 289 4.0E-32
7 g657.t5 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 295 415 3.71E-30
9 g657.t5 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 434 575 2.23E-41
16 g657.t5 TIGRFAM TIGR00617 rpa1: replication factor-a protein 1 (rpa1) 7 575 1.9E-176

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