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.t3 TTS g657.t3 5028704 5028704
chr_3 g657 g657.t3 isoform g657.t3 5028786 5030818
chr_3 g657 g657.t3 exon g657.t3.exon1 5028786 5028902
chr_3 g657 g657.t3 cds g657.t3.CDS1 5028786 5028902
chr_3 g657 g657.t3 exon g657.t3.exon2 5028969 5030397
chr_3 g657 g657.t3 cds g657.t3.CDS2 5028969 5030397
chr_3 g657 g657.t3 exon g657.t3.exon3 5030454 5030818
chr_3 g657 g657.t3 cds g657.t3.CDS3 5030454 5030569
chr_3 g657 g657.t3 TSS g657.t3 5030951 5030951

Sequences

>g657.t3 Gene=g657 Length=1911
ATGGCAAAATATTTGACGAAGTTGTCAGTTGGAAAATTGGCTGTAAGTATAAATTAAAAA
TATTTCACAATCTCTTGCAAAAAAATTATAAAATGTTTTCTTTTTCTCTAGAGAATCGTT
CAAGGAGAAGATTGCCCTTGTCCTCTTGTCTTTCAAGTAATTGGTTCAAAGAGAGTGCAA
TCAACTTCAGATGCACCAGATCGTTGTCGCTTAGTTTTGAATGATGGTGTAACTCAACAT
GGATTTGCAATGTTATCTGCAAATTTAAATGGAAGATACGCTAATGGAGAGTTTGATGAT
TACTCAATCATTCGTATCGATCGTTTTGTACCTTCACGAGTTAATCGCAATAATCCGAAT
GATAAAAATGTCATCATTTTGTTTGATATCGAGACTTTACACAGTGGAAAAGAAGTTGGT
GAACCCATTTCTGCAAATTCTGAATCACTTTCATCATCATCATCATCAAATTCTGTTCCT
GCACCTCAAAAAGAAAATGTCAATACAAATACAAATTCACGATATTCAACATCTGCAAAT
AACCCAAATACATCTTTAAATCTTAATTCAAGTATGGCAGGTGATTTGAGTGAACATCTC
ACAATGCCAATCGATTCATTGAGTCCTTATCAAAATAAGTGGGTAATTAAGGCTCGTGTT
ACAGCAAAGTCATCAATTCGTTCTTGGAAGAATGAAAAAGGCGAAGGAAAACTCTTTAAC
GTTGATCTTTGTGATGAATCTGGTGAAATTCGATGCACTGGTTTTCGTGATTCAGTTGAT
CGTTTCTATGATTTACTTGAAATTGGCAAGGTTTATTATATTAGCAAATGCCAGTTGAAA
CCAGCAAACAAGAAATATTCAAAAATCAACAATGATTATGAGATGACAATGTCTAGTGAA
ACTCAAATTCAGCCTTGTTCTGATGACACATCGAGTATTCCAAAAATCAAATATAATCTT
GTTTCGATTTCTGATTTGGCAGGAAAACCTAAGGATGACATTGTTGATGTAATTGGTATT
GCTCGTGAAATAGGACAAGTCACTAATATTGTTGCACGGGCATCTGGGCAGCAACTAACT
AAACGAGAAGTCACCATTGCTGATCAAACAAACGCATCAATTGTTCTTACCTTATGGGGC
GCTGAGGCCGAAAATTTTTCTGGTTTTGATAATCCTGTAGTTTTAGCTAAGAATGTAAGA
ATTGGCGAATATGGTGGTGGTAAAACATTGGGAACAACTGTAAGCTCAACTGTTTTAGTA
AATCCTGAGATGCCTGAAGCACATCAATTGAAAGGCTGGTATGATAACAATGCTTCAAAA
TGTTCATTCGTTGGTTTATCACAACGCACAGCAGGTCCAAGCTCAGCTTATCAATGGGCT
ACTTTCAATGATTGCTTGAAGAAACAATTTGGTATTGATAAGGCTGATTATTTCCAAACA
ATGGCGATGATTCACATGATTCGTATTGAAAACATGTTCTACAAAGCTTGCCCAAGTGAA
AGTTGCAACAAGAAAGTAATTGATTCTGGAAATGGCGTGTATCGATGTGAGAAATGTAAC
GCTGAATCGCCAAATTATTCTAATCGTATGCTGGCTAATGTATTACTTGGTGACTCAACT
TCAAATCGTTGGGTTACTCTTTTTGCTAATGTCGGAGAAAAACTTTTTGGCAAGAATACT
GATGAATTGGTAAGAATCAAAGAAAATGATAAGAATGAGTTTGACAATTTGATACAAAAG
ATACTCTTCAAACCTCAAATTTATAAATTGCGTACCCAAACTGAGACATACAATGATGTA
CCACGAAACAAGATCACTTGTGTTGCTGTTGGAGAAACAAAAATTAAAGATTATAATCAG
CATTTGCTTGCAAACATTCAACGTTTGACTGGAATCTGCGTTGATAAATAA

>g657.t3 Gene=g657 Length=553
MLSANLNGRYANGEFDDYSIIRIDRFVPSRVNRNNPNDKNVIILFDIETLHSGKEVGEPI
SANSESLSSSSSSNSVPAPQKENVNTNTNSRYSTSANNPNTSLNLNSSMAGDLSEHLTMP
IDSLSPYQNKWVIKARVTAKSSIRSWKNEKGEGKLFNVDLCDESGEIRCTGFRDSVDRFY
DLLEIGKVYYISKCQLKPANKKYSKINNDYEMTMSSETQIQPCSDDTSSIPKIKYNLVSI
SDLAGKPKDDIVDVIGIAREIGQVTNIVARASGQQLTKREVTIADQTNASIVLTLWGAEA
ENFSGFDNPVVLAKNVRIGEYGGGKTLGTTVSSTVLVNPEMPEAHQLKGWYDNNASKCSF
VGLSQRTAGPSSAYQWATFNDCLKKQFGIDKADYFQTMAMIHMIRIENMFYKACPSESCN
KKVIDSGNGVYRCEKCNAESPNYSNRMLANVLLGDSTSNRWVTLFANVGEKLFGKNTDEL
VRIKENDKNEFDNLIQKILFKPQIYKLRTQTETYNDVPRNKITCVAVGETKIKDYNQHLL
ANIQRLTGICVDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g657.t3 CDD cd04474 RPA1_DBD_A 120 222 1.1429E-51
15 g657.t3 CDD cd04475 RPA1_DBD_B 251 352 1.99139E-37
16 g657.t3 CDD cd04476 RPA1_DBD_C 390 543 4.50242E-49
10 g657.t3 Gene3D G3DSA:2.40.50.140 - 1 65 3.0E-7
13 g657.t3 Gene3D G3DSA:2.40.50.140 - 118 226 2.4E-42
11 g657.t3 Gene3D G3DSA:2.40.50.140 - 228 362 4.6E-39
12 g657.t3 Gene3D G3DSA:2.40.50.140 - 363 546 1.8E-49
9 g657.t3 MobiDBLite mobidb-lite consensus disorder prediction 61 101 -
4 g657.t3 PANTHER PTHR23273 REPLICATION FACTOR A 1, RFA1 1 542 1.6E-91
5 g657.t3 PANTHER PTHR23273:SF47 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBUNIT A 1 542 1.6E-91
1 g657.t3 Pfam PF01336 OB-fold nucleic acid binding domain 131 211 4.0E-13
2 g657.t3 Pfam PF16900 Replication protein A OB domain 240 338 8.4E-26
3 g657.t3 Pfam PF08646 Replication factor-A C terminal domain 394 539 8.3E-44
8 g657.t3 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 119 229 3.71E-32
6 g657.t3 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 235 355 3.43E-30
7 g657.t3 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 374 546 3.77E-48
14 g657.t3 TIGRFAM TIGR00617 rpa1: replication factor-a protein 1 (rpa1) 1 544 1.9E-172

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