General information for g5205.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA repair and recombination protein RAD54-like.
Parent gene
- The parent gene g5205 is located on chr_2: 7642584..7644588 (- 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_2 | g5205 | g5205.t2 | TTS | g5205.t2 | 7641621 | 7641621 |
| chr_2 | g5205 | g5205.t2 | isoform | g5205.t2 | 7642584 | 7644588 |
| chr_2 | g5205 | g5205.t2 | exon | g5205.t2.exon1 | 7642584 | 7643559 |
| chr_2 | g5205 | g5205.t2 | cds | g5205.t2.CDS1 | 7642584 | 7643559 |
| chr_2 | g5205 | g5205.t2 | exon | g5205.t2.exon2 | 7643702 | 7643799 |
| chr_2 | g5205 | g5205.t2 | cds | g5205.t2.CDS2 | 7643702 | 7643751 |
| chr_2 | g5205 | g5205.t2 | exon | g5205.t2.exon3 | 7643849 | 7644588 |
| chr_2 | g5205 | g5205.t2 | TSS | g5205.t2 | 7644654 | 7644654 |
Sequences
>g5205.t2 Gene=g5205 Length=1814
ATGGTAATAACACAAATAATTAAACATTTAAAATAGTTTCTAAGGTTCTTTATTTATTTT
TAGCATCGGAAACCAGTTCCTAAATTTGTTCCTTTTGCGAGCAAAAAAGAATTTAAACCA
CCATTGCTTGATCAATCGTCTGAACTTAATCAATCACCATTACACAAAAATTCAGTGCCT
AAATTCGTGCCTTATGAAAATAAAAAGCCTTTTAAGCCGCCTTTACTTGAAAATCCAAAA
TCAGAGAGAAAAGCTCGTAAAACAAAAGCAAAAGATGAAAATGAAGTCATACCATGGAAG
CCATTTAAAATTTCAATTACTGATCATGAAGATATGATAACAAAGATATTGAATAAGGCA
TTCAAAGTACCAATTCCAGGCTATATCGATGAATATACTACTAAAACTCTTGGAATGCGA
AAAGTCTTTGTTAGAAGGTAATTTTCTTAATACATTTTGAAGTGATGATTTTCTACGTTT
TCATAATTTTAGGCCACTTCATGATCCTAAAGCTTGTAATGCTTTAGTACTTTATGAACC
TGTGATAAAAGAACCAGAAAAAGCTAGTACAAAGAACACTTCTTTATATTATCAAAAAGT
TAGATTTGCTGATCATGACAATCATCCGGTTCATGTTGTTTGTGATCCTGTATTGAGTAA
CATTTTAAGACCGCATCAGAGAGAAGGTGTAAAATTTATGTATGATTGCGTAACTGGAGC
AAAAGGGGATTTCAATGGCTTACCAATATGTTAATAAAATAAATTTTAGGTCTTGGTAAA
ACACTTCAATGCATCACACTTGTTTGGACATTATTGAGGCAAAGCCCAGACTGCAAACTA
CTTATATGGCAAATAAAAGTGCTAGATGTGGTTCTCCCGTTCTAATTATCAGTTACGAAA
CCTTCCGTCTTTATTCTCACATTTTAAATGCATCCGAAGTCGGACTTGTATTATGTGATG
AAGGACATCGTTTAAAGAATTGTGAAAATCAAACATATCAAGCTTTAATGGGACTTCAAA
CAAAAAAGCGTGTGTTGCTTTCAGGCACACCTATACAAAACGATCTCTCAGAATATTATA
GTTTAGTGCACTTTGTTAATCCTGGCATGTTAGGAACAAATAATGAATTTAAACGTCAAT
TTGAAAATGTAATTTTAAAAGGACAAGATGCTTGTAGCACTGATAAAGAACGTGAAAAAG
CAAATGAGCGTCTTCAAGAATTGACTGCACTTGTTAATCAATGTATGATTCGTCGTACAA
GTAATTTACTTACAAAATATCTACCAATTAAATTTGAAATGGTTGTTTGCGTGAAATTGA
CTCAACTACAAGTGGACATCTATCGAAGTTTCCTTAAATCAGACACTATTCGCCGATCGA
TGATGAACAATGCAACTGGTGAAAAAGGAAGTGCACGCGTTTTAGCCAACATTACATCAC
TAAAGAAACTTTGCAGTCATCCCGAACTTGTTATTGACAAAATAAACGAACGTTCTGAAG
GATTTGAAGATGCTGGACAATATTTACCTAATGAATGGAGTAGTCGTGAATTATTGCCTC
AATTTGGTGGAAAAGTTCTATTGCTTGATGTTATGCTGGCACAAATCAAAGCAACTACAA
ATGACAAACTCGTACTAGTCTCTAATTACACACAAACACTTGATCTCTTTGAAAAATTAT
GCCGAAAACGTGGATATCAATACTGTCGTCTTGATGGAACAATGTCAATTAAAAAGCGAG
GAAAAATGGTTGAAGATTTCAACAAACCAGATTCTTCTCTCTTTATTTTCATGCTTAGTT
CAAAAGCTGGAGGT
>g5205.t2 Gene=g5205 Length=342
MHHTCLDIIEAKPRLQTTYMANKSARCGSPVLIISYETFRLYSHILNASEVGLVLCDEGH
RLKNCENQTYQALMGLQTKKRVLLSGTPIQNDLSEYYSLVHFVNPGMLGTNNEFKRQFEN
VILKGQDACSTDKEREKANERLQELTALVNQCMIRRTSNLLTKYLPIKFEMVVCVKLTQL
QVDIYRSFLKSDTIRRSMMNNATGEKGSARVLANITSLKKLCSHPELVIDKINERSEGFE
DAGQYLPNEWSSRELLPQFGGKVLLLDVMLAQIKATTNDKLVLVSNYTQTLDLFEKLCRK
RGYQYCRLDGTMSIKKRGKMVEDFNKPDSSLFIFMLSSKAGG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5205.t2 | CDD | cd18793 | SF2_C_SNF | 261 | 342 | 3.0551E-24 |
| 9 | g5205.t2 | Coils | Coil | Coil | 135 | 155 | - |
| 7 | g5205.t2 | Gene3D | G3DSA:3.40.50.10810 | - | 4 | 155 | 7.9E-47 |
| 8 | g5205.t2 | Gene3D | G3DSA:1.20.120.850 | - | 178 | 257 | 6.5E-18 |
| 3 | g5205.t2 | PANTHER | PTHR45629:SF7 | DNA EXCISION REPAIR PROTEIN ERCC-6-RELATED | 22 | 342 | 3.2E-106 |
| 4 | g5205.t2 | PANTHER | PTHR45629 | SNF2/RAD54 FAMILY MEMBER | 22 | 342 | 3.2E-106 |
| 2 | g5205.t2 | Pfam | PF00176 | SNF2 family N-terminal domain | 29 | 228 | 1.9E-36 |
| 1 | g5205.t2 | Pfam | PF00271 | Helicase conserved C-terminal domain | 272 | 332 | 6.4E-6 |
| 11 | g5205.t2 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 1 | 106 | 12.98 |
| 10 | g5205.t2 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 265 | 342 | 7.337 |
| 5 | g5205.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 23 | 156 | 4.7E-30 |
| 6 | g5205.t2 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 160 | 342 | 1.2E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5205/g5205.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5205.t2.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005524 | ATP binding | MF |
| GO:0070615 | NA | NA |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed