Gene loci information

Transcript annotation

  • This transcript has been annotated as Replication factor C subunit 1.

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_1 g11763 g11763.t1 TSS g11763.t1 18275206 18275206
chr_1 g11763 g11763.t1 isoform g11763.t1 18275303 18277508
chr_1 g11763 g11763.t1 exon g11763.t1.exon1 18275303 18275311
chr_1 g11763 g11763.t1 cds g11763.t1.CDS1 18275303 18275311
chr_1 g11763 g11763.t1 exon g11763.t1.exon2 18275373 18275904
chr_1 g11763 g11763.t1 cds g11763.t1.CDS2 18275373 18275904
chr_1 g11763 g11763.t1 exon g11763.t1.exon3 18275960 18276537
chr_1 g11763 g11763.t1 cds g11763.t1.CDS3 18275960 18276537
chr_1 g11763 g11763.t1 exon g11763.t1.exon4 18276609 18277508
chr_1 g11763 g11763.t1 cds g11763.t1.CDS4 18276609 18277508
chr_1 g11763 g11763.t1 TTS g11763.t1 18277588 18277588

Sequences

>g11763.t1 Gene=g11763 Length=2019
ATGTCAAAGGACATTAGATCATTCTTTAAAATTGACAACTCAAAAAAACGAAAAAATGAA
AGTAATATTTCATCAATTGAAAAAAGACAAAAATTATTGATAAATAAGCTTGTTGCTAAT
GATACTAATATTGATACAAAAGATAATATTGCTAAAAATGATAATATTGCTACAAAAGAT
GATATTATTTCTAAAGATGAAATTGTTCTTAAAAATGATATTATTCCTAAAGATGATATC
CCTAAAAATAATATTGTTCCAAAAGTTAATATTGATACTAATGGTAATGATACAAATACA
AAACCAAGTTTACCAAAAAACGATAGTTATGAATATTCATTTGTTGATAAATATGCACCA
ACTTCAATGAAACAAATTATCGGCCAACAAGGCGGACAAAGTAATGCACATAAATTGCAA
CAATGGCTTTTGAATTGGCATAAAAATCATGGTGATTCTAATAAAAAAATAAAAGTAAAT
CCAAGAAGCAATGATAGCAGTTCAATGAAAGCTGCATTACTATCCGGCCAACCTGGAATA
GGGAAGACAACAACTGCACATTTGGTTGCTAAAGAGTGTTTGTTTGATGTAGTAGAATTC
AATGCATCTGATACGAGAAGCAAGAAATTACTCAAAGAGGAAGTTTCTCAGTTGCTTGCA
AATAAATCATTAAAAGGATATTTAACTGGCAATGAGAAGACTGTTTCCAATAGGCATGTA
TTGATTATGGATGAAGTTGATGGTTGTGCCGGAAATGAGGATCGTGGAGGAATTGCTGAA
TTAATTCAATTGATAAAGGAATCTAAAATTCCCATTATATGCATGTGTAATGATCGTTCG
CACCCAAAAATTAGGTCTTTGGTTAATTACTGTTTTGATTTGAGATTTCAAAAACCAACA
ACTAATCAGATTAGAGGTTTAGTAATGAGTATTTGTTTTAAAGAAGGAATAAAAATGGAA
CCTGCTGCAGCCGAAGCTCTGATAACTGGCACAGGAAATGACATACGTCAAACATTGAAT
CATCTTGCTCTATATAGTGCAGGAAAGAAAAGTGATCAAAAAATCAGTGCTGATGATGCG
AAAAAGAATGCTCAAATGGCTGAAAAAGATGTTAAAATTGGACCATGGGATGTTATTCGT
AAAGTATTTTCTGCTGATGAACATAGAACTATGTCTTTCAATGATAAAAGTGATCTTTTT
TTCTATGACTATAATATTGCACCGCTTTTTGTTCAAGAAAATTACTTATGCGTAAAACCA
GAAGGTAAAGCTAATCAAATCTTATCGAAGGTAGCAAAAACGGCAGACTCATTAAGTTTA
GGTGATATGGTCGAAAGAAAAATTCGTTCAAATATGGCGTGGTCTCTGTTACCAACACAG
GCTATATTCAGCTCTGTTTTGCCGGGTGAATATATGAAAGGAAATTTCATGAAATCTCCA
TCATTTCCATCATGGTTAGGAAAAAATTCAAAAAGTCAGAAACAAAAAAGATTAGCACAA
GAACTTCATGATCACACGAGAATTGTTACGTCTGGTTCTCGTATGGCTATTCGCTTGGAT
TATAGTCAATTTTTAATAAAAGCTATTACTAGTCCATTACAAGAAAAAGGACTTGATGGA
GTCTCTGAATCACTTGATGTTATTAAATCTTATCATTTGCTTCGTGAAGATATCGAGTCA
TTGCTTGAAATAACGACATGGGGTTCAACTAAAAATCTTTGGGATCAAATTGACAGCAAA
GTTAAAGCTGCGCTTACTAGAGCTTACAATAAAGAAATTCGCCCATATTCCTATTCTGTA
CAAGCAGGTGTAAAGAAAAAGAGAACCGCCAATTTTGATATTGAAGGATATGGCGATGAG
AATATAGAAAATTCTGATCAAGAAGAAGACGAAGAGTCAATAGAAAGTAGTAATTTGATA
AAAGTTAAAAAAACAGCATCTCTACCAAAAAATAAAGTAAACTCGACTAAGGCTACTGTT
GCAAAGACCAATAGCAGTAAAGGAAAGGGAAACAAATGA

>g11763.t1 Gene=g11763 Length=672
MSKDIRSFFKIDNSKKRKNESNISSIEKRQKLLINKLVANDTNIDTKDNIAKNDNIATKD
DIISKDEIVLKNDIIPKDDIPKNNIVPKVNIDTNGNDTNTKPSLPKNDSYEYSFVDKYAP
TSMKQIIGQQGGQSNAHKLQQWLLNWHKNHGDSNKKIKVNPRSNDSSSMKAALLSGQPGI
GKTTTAHLVAKECLFDVVEFNASDTRSKKLLKEEVSQLLANKSLKGYLTGNEKTVSNRHV
LIMDEVDGCAGNEDRGGIAELIQLIKESKIPIICMCNDRSHPKIRSLVNYCFDLRFQKPT
TNQIRGLVMSICFKEGIKMEPAAAEALITGTGNDIRQTLNHLALYSAGKKSDQKISADDA
KKNAQMAEKDVKIGPWDVIRKVFSADEHRTMSFNDKSDLFFYDYNIAPLFVQENYLCVKP
EGKANQILSKVAKTADSLSLGDMVERKIRSNMAWSLLPTQAIFSSVLPGEYMKGNFMKSP
SFPSWLGKNSKSQKQKRLAQELHDHTRIVTSGSRMAIRLDYSQFLIKAITSPLQEKGLDG
VSESLDVIKSYHLLREDIESLLEITTWGSTKNLWDQIDSKVKAALTRAYNKEIRPYSYSV
QAGVKKKRTANFDIEGYGDENIENSDQEEDEESIESSNLIKVKKTASLPKNKVNSTKATV
AKTNSSKGKGNK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11763.t1 CDD cd00009 AAA 165 296 2.59037E-13
12 g11763.t1 CDD cd18140 HLD_clamp_RFC 299 362 1.5636E-11
7 g11763.t1 Gene3D G3DSA:3.40.50.300 - 112 298 3.0E-51
9 g11763.t1 Gene3D G3DSA:1.10.8.60 - 299 373 7.8E-21
8 g11763.t1 Gene3D G3DSA:1.20.272.10 - 374 482 1.9E-35
16 g11763.t1 MobiDBLite mobidb-lite consensus disorder prediction 617 672 -
14 g11763.t1 MobiDBLite mobidb-lite consensus disorder prediction 619 633 -
15 g11763.t1 MobiDBLite mobidb-lite consensus disorder prediction 639 672 -
3 g11763.t1 PANTHER PTHR23389 CHROMOSOME TRANSMISSION FIDELITY FACTOR 18 83 657 8.5E-186
4 g11763.t1 PANTHER PTHR23389:SF6 REPLICATION FACTOR C SUBUNIT 1 83 657 8.5E-186
10 g11763.t1 PIRSF PIRSF036578 RFC1 10 672 2.4E-217
1 g11763.t1 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 173 297 3.4E-13
2 g11763.t1 Pfam PF08519 Replication factor RFC1 C terminal domain 439 591 2.1E-53
13 g11763.t1 SMART SM00382 AAA_5 168 302 7.5E-7
6 g11763.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 114 363 3.91E-31
5 g11763.t1 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like 373 507 9.69E-47

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:0005663 DNA replication factor C complex CC
GO:0003677 DNA binding MF
GO:0006281 DNA repair BP
GO:0005524 ATP binding MF
GO:0003689 DNA clamp loader activity MF
GO:0006260 DNA replication BP
GO:0016887 ATP hydrolysis activity 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