General information for g11810.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Replication factor C subunit 4.
Parent gene
- The parent gene g11810 is located on chr_1: 18527567..18528478 (+ strand)
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 | g11810 | g11810.t1 | TSS | g11810.t1 | 18526227 | 18526227 |
| chr_1 | g11810 | g11810.t1 | isoform | g11810.t1 | 18526296 | 18527567 |
| chr_1 | g11810 | g11810.t1 | exon | g11810.t1.exon1 | 18526296 | 18526406 |
| chr_1 | g11810 | g11810.t1 | cds | g11810.t1.CDS1 | 18526296 | 18526406 |
| chr_1 | g11810 | g11810.t1 | exon | g11810.t1.exon2 | 18526478 | 18526589 |
| chr_1 | g11810 | g11810.t1 | cds | g11810.t1.CDS2 | 18526478 | 18526589 |
| chr_1 | g11810 | g11810.t1 | exon | g11810.t1.exon3 | 18526647 | 18526736 |
| chr_1 | g11810 | g11810.t1 | cds | g11810.t1.CDS3 | 18526647 | 18526736 |
| chr_1 | g11810 | g11810.t1 | exon | g11810.t1.exon4 | 18526792 | 18527567 |
| chr_1 | g11810 | g11810.t1 | cds | g11810.t1.CDS4 | 18526792 | 18527567 |
| chr_1 | g11810 | g11810.t1 | TTS | g11810.t1 | 18527649 | 18527649 |
Sequences
>g11810.t1 Gene=g11810 Length=1089
ATGCAAGCATTTTTACAAGGCCATAAATTGTCAGCTCAAAAACCAGCTTCATTTAATAGT
CAGAGAAAAGAGAAAAAGAGTCGAGAAAAGCCGATTCCTTGGGTAGAAAAGTATCGGCCA
AAGAAAGTTGATGATGTTGTAGAGCAAAATGAAGTGTGTGCTGTTCTGAGAGAAAGTATG
CAAACTTCAGACTTACCTAATTTATTATTATATGGTCCTCCAGGCACTGGAAAAACATCG
ACAATCTTAGCAGCAGCTCGTCAACTTTTTGGTGAATTTATAAAAGAACGTGTGCTTGAG
CTTAATGCATCAGATGATCGTGGAATTTCGGTTATAAGAACAAAAGTTAAAAATTTTGCA
CAACTTAAAGCGAGTAATATCCGACCAGATGGAAAACCATGTCCACCTTTCAAGATAATC
ATTCTTGATGAAGCAGATGCAATGACAAATGCTGCTCAAGCTGCCTTACGTCGTACAATG
GAAAAAGAAACTCGCACTACAAGATTCTGTTTGATTTGCAACTATGTATCAAAAATAATA
GAACCAATCACATCACGATGTACTAAATTTCGATTTATTCCATTGCATGAGGAAAAAATC
ATTGAGAGACTAAAGTTTATTGCTGAACAAGAAAAATTCAATATTGAAGATGAAGCATTA
AAAAGTATAGTCGAAACTTCAAATGGAGACCTCAGAAAGGCAATAACAACGCTTCAATCA
TGTTATCGATTAAAATGTGGATCAGACATAAAACATAGTCAAGTTACGCTTTTAGATGTT
TTTGAAATGTCTGGAATTGTACCTGATTCATATTTAGAAGAGTTCATAAAAGTCGTAAAA
AGTAAGGAACTTCAAGCACTGGAAAATTTTATAGATGCTTTTACTTATGAAGCATACAGT
CTCTCACAATTCTTTGATCAACTTAGCATCAAAATTATCATGGATGAAACTATTACAAAC
AATCAAAAAGCTATAATTCTCGATAAATTAGGAGAGTCATCTTTTCGACTTTCAACTGGA
GGCAGTGAATATCTTCAATTAATTGATTTTGGTACAATTTGTATCATTGCATTTTCAAAA
CAAAATTAA
>g11810.t1 Gene=g11810 Length=362
MQAFLQGHKLSAQKPASFNSQRKEKKSREKPIPWVEKYRPKKVDDVVEQNEVCAVLRESM
QTSDLPNLLLYGPPGTGKTSTILAAARQLFGEFIKERVLELNASDDRGISVIRTKVKNFA
QLKASNIRPDGKPCPPFKIIILDEADAMTNAAQAALRRTMEKETRTTRFCLICNYVSKII
EPITSRCTKFRFIPLHEEKIIERLKFIAEQEKFNIEDEALKSIVETSNGDLRKAITTLQS
CYRLKCGSDIKHSQVTLLDVFEMSGIVPDSYLEEFIKVVKSKELQALENFIDAFTYEAYS
LSQFFDQLSIKIIMDETITNNQKAIILDKLGESSFRLSTGGSEYLQLIDFGTICIIAFSK
QN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11810.t1 | CDD | cd00009 | AAA | 47 | 195 | 1.264E-22 |
| 13 | g11810.t1 | CDD | cd18140 | HLD_clamp_RFC | 195 | 245 | 1.53503E-17 |
| 9 | g11810.t1 | Gene3D | G3DSA:3.40.50.300 | - | 20 | 195 | 1.4E-51 |
| 11 | g11810.t1 | Gene3D | G3DSA:1.10.8.60 | - | 196 | 266 | 1.2E-19 |
| 10 | g11810.t1 | Gene3D | G3DSA:1.20.272.10 | - | 267 | 355 | 7.6E-20 |
| 8 | g11810.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 31 | - |
| 3 | g11810.t1 | PANTHER | PTHR11669:SF20 | REPLICATION FACTOR C SUBUNIT 4 | 24 | 350 | 2.5E-120 |
| 4 | g11810.t1 | PANTHER | PTHR11669 | REPLICATION FACTOR C / DNA POLYMERASE III GAMMA-TAU SUBUNIT | 24 | 350 | 2.5E-120 |
| 1 | g11810.t1 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 68 | 194 | 1.8E-16 |
| 2 | g11810.t1 | Pfam | PF08542 | Replication factor C C-terminal domain | 268 | 350 | 1.4E-9 |
| 7 | g11810.t1 | SMART | SM00382 | AAA_5 | 64 | 198 | 5.2E-12 |
| 6 | g11810.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 32 | 243 | 7.71E-48 |
| 5 | g11810.t1 | SUPERFAMILY | SSF48019 | post-AAA+ oligomerization domain-like | 267 | 351 | 5.53E-14 |
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:0003677 | DNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006260 | DNA replication | BP |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10755 (replication factor C subunit 2/4)
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.
