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.t1 TTS g657.t1 5028704 5028704
chr_3 g657 g657.t1 isoform g657.t1 5028786 5030818
chr_3 g657 g657.t1 exon g657.t1.exon1 5028786 5028902
chr_3 g657 g657.t1 cds g657.t1.CDS1 5028786 5028902
chr_3 g657 g657.t1 exon g657.t1.exon2 5028969 5030397
chr_3 g657 g657.t1 cds g657.t1.CDS2 5028969 5030397
chr_3 g657 g657.t1 exon g657.t1.exon3 5030454 5030707
chr_3 g657 g657.t1 cds g657.t1.CDS3 5030454 5030707
chr_3 g657 g657.t1 exon g657.t1.exon4 5030777 5030818
chr_3 g657 g657.t1 cds g657.t1.CDS4 5030777 5030818
chr_3 g657 g657.t1 TSS g657.t1 5030951 5030951

Sequences

>g657.t1 Gene=g657 Length=1842
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
AAACCTCAAATTTATAAATTGCGTACCCAAACTGAGACATACAATGATGTACCACGAAAC
AAGATCACTTGTGTTGCTGTTGGAGAAACAAAAATTAAAGATTATAATCAGCATTTGCTT
GCAAACATTCAACGTTTGACTGGAATCTGCGTTGATAAATAA

>g657.t1 Gene=g657 Length=613
MAKYLTKLSVGKLARIVQGEDCPCPLVFQVIGSKRVQSTSDAPDRCRLVLNDGVTQHGFA
MLSANLNGRYANGEFDDYSIIRIDRFVPSRVNRNNPNDKNVIILFDIETLHSGKEVGEPI
SANSESLSSSSSSNSVPAPQKENVNTNTNSRYSTSANNPNTSLNLNSSMAGDLSEHLTMP
IDSLSPYQNKWVIKARVTAKSSIRSWKNEKGEGKLFNVDLCDESGEIRCTGFRDSVDRFY
DLLEIGKVYYISKCQLKPANKKYSKINNDYEMTMSSETQIQPCSDDTSSIPKIKYNLVSI
SDLAGKPKDDIVDVIGIAREIGQVTNIVARASGQQLTKREVTIADQTNASIVLTLWGAEA
ENFSGFDNPVVLAKNVRIGEYGGGKTLGTTVSSTVLVNPEMPEAHQLKGWYDNNASKCSF
VGLSQRTAGPSSAYQWATFNDCLKKQFGIDKADYFQTMAMIHMIRIENMFYKACPSESCN
KKVIDSGNGVYRCEKCNAESPNYSNRMLANVLLGDSTSNRWVTLFANVGEKLFGKNTDEL
VRIKENDKNEFDNLIQKILFKPQIYKLRTQTETYNDVPRNKITCVAVGETKIKDYNQHLL
ANIQRLTGICVDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g657.t1 CDD cd04474 RPA1_DBD_A 180 282 4.46974E-52
17 g657.t1 CDD cd04475 RPA1_DBD_B 311 412 1.89538E-37
18 g657.t1 CDD cd04476 RPA1_DBD_C 450 603 6.63912E-49
13 g657.t1 Gene3D G3DSA:2.40.50.140 - 6 125 1.0E-21
14 g657.t1 Gene3D G3DSA:2.40.50.140 - 178 286 2.8E-42
15 g657.t1 Gene3D G3DSA:2.40.50.140 - 288 422 5.5E-39
12 g657.t1 Gene3D G3DSA:2.40.50.140 - 423 606 2.3E-49
11 g657.t1 MobiDBLite mobidb-lite consensus disorder prediction 121 161 -
5 g657.t1 PANTHER PTHR23273 REPLICATION FACTOR A 1, RFA1 7 602 2.1E-96
6 g657.t1 PANTHER PTHR23273:SF47 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT A 7 602 2.1E-96
3 g657.t1 Pfam PF04057 Replication factor-A protein 1, N-terminal domain 8 111 8.8E-14
1 g657.t1 Pfam PF01336 OB-fold nucleic acid binding domain 191 271 4.6E-13
2 g657.t1 Pfam PF16900 Replication protein A OB domain 300 398 9.9E-26
4 g657.t1 Pfam PF08646 Replication factor-A C terminal domain 454 599 1.0E-43
9 g657.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 7 120 2.4E-16
8 g657.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 179 289 4.28E-32
7 g657.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 295 415 4.0E-30
10 g657.t1 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 434 606 4.63E-48
16 g657.t1 TIGRFAM TIGR00617 rpa1: replication factor-a protein 1 (rpa1) 7 604 4.2E-183

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