General information for g5205.t1
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.t1 | TTS | g5205.t1 | 7641621 | 7641621 |
| chr_2 | g5205 | g5205.t1 | isoform | g5205.t1 | 7641897 | 7644588 |
| chr_2 | g5205 | g5205.t1 | exon | g5205.t1.exon1 | 7641897 | 7642224 |
| chr_2 | g5205 | g5205.t1 | cds | g5205.t1.CDS1 | 7641897 | 7642224 |
| chr_2 | g5205 | g5205.t1 | exon | g5205.t1.exon2 | 7642285 | 7643770 |
| chr_2 | g5205 | g5205.t1 | cds | g5205.t1.CDS2 | 7642285 | 7643770 |
| chr_2 | g5205 | g5205.t1 | exon | g5205.t1.exon3 | 7643828 | 7644096 |
| chr_2 | g5205 | g5205.t1 | cds | g5205.t1.CDS3 | 7643828 | 7644096 |
| chr_2 | g5205 | g5205.t1 | exon | g5205.t1.exon4 | 7644152 | 7644525 |
| chr_2 | g5205 | g5205.t1 | cds | g5205.t1.CDS4 | 7644152 | 7644525 |
| chr_2 | g5205 | g5205.t1 | exon | g5205.t1.exon5 | 7644586 | 7644588 |
| chr_2 | g5205 | g5205.t1 | cds | g5205.t1.CDS5 | 7644586 | 7644588 |
| chr_2 | g5205 | g5205.t1 | TSS | g5205.t1 | 7644654 | 7644654 |
Sequences
>g5205.t1 Gene=g5205 Length=2460
ATGCATCGGAAACCAGTTCCTAAATTTGTTCCTTTTGCGAGCAAAAAAGAATTTAAACCA
CCATTGCTTGATCAATCGTCTGAACTTAATCAATCACCATTACACAAAAATTCAGTGCCT
AAATTCGTGCCTTATGAAAATAAAAAGCCTTTTAAGCCGCCTTTACTTGAAAATCCAAAA
TCAGAGAGAAAAGCTCGTAAAACAAAAGCAAAAGATGAAAATGAAGTCATACCATGGAAG
CCATTTAAAATTTCAATTACTGATCATGAAGATATGATAACAAAGATATTGAATAAGGCA
TTCAAAGTACCAATTCCAGGCTATATCGATGAATATACTACTAAAACTCTTGGAATGCGA
AAAGTCTTTGTTAGAAGGCCACTTCATGATCCTAAAGCTTGTAATGCTTTAGTACTTTAT
GAACCTGTGATAAAAGAACCAGAAAAAGCTAGTACAAAGAACACTTCTTTATATTATCAA
AAAGTTAGATTTGCTGATCATGACAATCATCCGGTTCATGTTGTTTGTGATCCTGTATTG
AGTAACATTTTAAGACCGCATCAGAGAGAAGGTGTAAAATTTATGTATGATTGCGTAACT
GGAGCAAAAGGGGATTTCAATGGCTGTATAATGGCAGATGAAATGGGTCTTGGTAAAACA
CTTCAATGCATCACACTTGTTTGGACATTATTGAGGCAAAGCCCAGACTGCAAACCTGAA
ATTATTAAAGCTATAATCGTTTGCCCTTCTTCTCTTGTGAAAAATTGGTATAATGAATTT
GGAAAATGGCTTGGAAATCGTGTCAATTGCTTGGCAATTTCAAATGAATCTAAGGAAAAG
ACAACTGAACTACTCACTACTTATATGGCAAATAAAAGTGCTAGATGTGGTTCTCCCGTT
CTAATTATCAGTTACGAAACCTTCCGTCTTTATTCTCACATTTTAAATGCATCCGAAGTC
GGACTTGTATTATGTGATGAAGGACATCGTTTAAAGAATTGTGAAAATCAAACATATCAA
GCTTTAATGGGACTTCAAACAAAAAAGCGTGTGTTGCTTTCAGGCACACCTATACAAAAC
GATCTCTCAGAATATTATAGTTTAGTGCACTTTGTTAATCCTGGCATGTTAGGAACAAAT
AATGAATTTAAACGTCAATTTGAAAATGTAATTTTAAAAGGACAAGATGCTTGTAGCACT
GATAAAGAACGTGAAAAAGCAAATGAGCGTCTTCAAGAATTGACTGCACTTGTTAATCAA
TGTATGATTCGTCGTACAAGTAATTTACTTACAAAATATCTACCAATTAAATTTGAAATG
GTTGTTTGCGTGAAATTGACTCAACTACAAGTGGACATCTATCGAAGTTTCCTTAAATCA
GACACTATTCGCCGATCGATGATGAACAATGCAACTGGTGAAAAAGGAAGTGCACGCGTT
TTAGCCAACATTACATCACTAAAGAAACTTTGCAGTCATCCCGAACTTGTTATTGACAAA
ATAAACGAACGTTCTGAAGGATTTGAAGATGCTGGACAATATTTACCTAATGAATGGAGT
AGTCGTGAATTATTGCCTCAATTTGGTGGAAAAGTTCTATTGCTTGATGTTATGCTGGCA
CAAATCAAAGCAACTACAAATGACAAACTCGTACTAGTCTCTAATTACACACAAACACTT
GATCTCTTTGAAAAATTATGCCGAAAACGTGGATATCAATACTGTCGTCTTGATGGAACA
ATGTCAATTAAAAAGCGAGGAAAAATGGTTGAAGATTTCAACAAACCAGATTCTTCTCTC
TTTATTTTCATGCTTAGTTCAAAAGCTGGAGGTTGTGGTCTCAATTTGATTGGTGCTAAT
AGATTGATCATGTTTGATCCTGATTGGAATCCGGCTAATGATGAACAAGCAATGGCTCGT
GTTTGGCGTGATGGTCAAAAGAAACCTTGCTATATTTATCGTTTTGTTGCAACTGGAACA
ATAGAAGAAAAGATTTTTCAACGACAAACGCATAAGAAGGCATTGAGTAATACAGTGGTT
GATAATGATGAAGGCGAACGACATTTTAGCATGAACGATCTGAAAGAGCTATTCAAACTT
GATGAAACTACAATTTCTGATACACATGATATTTTTAAATGCAAACGTTGTATTAATAAT
GTGCAAACGACACTTCCTCCTGAAGGTTCTGATTGTACGAGTGATTTAAGTCAATGGTTC
CATTGCTCAAATAATCAAGGAATACCAGATGAAATTTTGACACAAGCATCTAAAATAACA
AACAACATTTCATTTGTCTTTCATCAACGCTCTGCACAAACAGAAGTAGAAACAGCAAAG
GCACAAGAAACAAAACCTAAAGAAAAGAAGCAGAAAATTATTTATGATGATGATGAATTC
ATAAATATAGATTCTGAGAGTGACAAAGACGATGATGATAGTGATGAAGACTACAAGTGA
>g5205.t1 Gene=g5205 Length=819
MHRKPVPKFVPFASKKEFKPPLLDQSSELNQSPLHKNSVPKFVPYENKKPFKPPLLENPK
SERKARKTKAKDENEVIPWKPFKISITDHEDMITKILNKAFKVPIPGYIDEYTTKTLGMR
KVFVRRPLHDPKACNALVLYEPVIKEPEKASTKNTSLYYQKVRFADHDNHPVHVVCDPVL
SNILRPHQREGVKFMYDCVTGAKGDFNGCIMADEMGLGKTLQCITLVWTLLRQSPDCKPE
IIKAIIVCPSSLVKNWYNEFGKWLGNRVNCLAISNESKEKTTELLTTYMANKSARCGSPV
LIISYETFRLYSHILNASEVGLVLCDEGHRLKNCENQTYQALMGLQTKKRVLLSGTPIQN
DLSEYYSLVHFVNPGMLGTNNEFKRQFENVILKGQDACSTDKEREKANERLQELTALVNQ
CMIRRTSNLLTKYLPIKFEMVVCVKLTQLQVDIYRSFLKSDTIRRSMMNNATGEKGSARV
LANITSLKKLCSHPELVIDKINERSEGFEDAGQYLPNEWSSRELLPQFGGKVLLLDVMLA
QIKATTNDKLVLVSNYTQTLDLFEKLCRKRGYQYCRLDGTMSIKKRGKMVEDFNKPDSSL
FIFMLSSKAGGCGLNLIGANRLIMFDPDWNPANDEQAMARVWRDGQKKPCYIYRFVATGT
IEEKIFQRQTHKKALSNTVVDNDEGERHFSMNDLKELFKLDETTISDTHDIFKCKRCINN
VQTTLPPEGSDCTSDLSQWFHCSNNQGIPDEILTQASKITNNISFVFHQRSAQTEVETAK
AQETKPKEKKQKIIYDDDEFINIDSESDKDDDDSDEDYK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5205.t1 | CDD | cd18793 | SF2_C_SNF | 530 | 656 | 3.22575E-57 |
| 11 | g5205.t1 | Coils | Coil | Coil | 404 | 424 | - |
| 8 | g5205.t1 | Gene3D | G3DSA:3.40.50.10810 | - | 151 | 424 | 3.1E-99 |
| 9 | g5205.t1 | Gene3D | G3DSA:3.40.50.300 | - | 425 | 725 | 1.5E-126 |
| 10 | g5205.t1 | Gene3D | G3DSA:1.20.120.850 | - | 447 | 703 | 1.5E-126 |
| 18 | g5205.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 21 | 72 | - |
| 16 | g5205.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 53 | 72 | - |
| 19 | g5205.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 776 | 819 | - |
| 15 | g5205.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 780 | 799 | - |
| 17 | g5205.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 800 | 819 | - |
| 4 | g5205.t1 | PANTHER | PTHR45629:SF7 | DNA EXCISION REPAIR PROTEIN ERCC-6-RELATED | 47 | 791 | 1.7E-213 |
| 5 | g5205.t1 | PANTHER | PTHR45629 | SNF2/RAD54 FAMILY MEMBER | 47 | 791 | 1.7E-213 |
| 2 | g5205.t1 | Pfam | PF08658 | Rad54 N terminal | 16 | 154 | 5.0E-11 |
| 3 | g5205.t1 | Pfam | PF00176 | SNF2 family N-terminal domain | 202 | 497 | 9.5E-58 |
| 1 | g5205.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 541 | 644 | 2.3E-16 |
| 21 | g5205.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 200 | 375 | 19.827 |
| 20 | g5205.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 534 | 695 | 16.315 |
| 14 | g5205.t1 | SMART | SM00487 | ultradead3 | 180 | 387 | 1.8E-37 |
| 13 | g5205.t1 | SMART | SM00490 | helicmild6 | 561 | 645 | 2.7E-22 |
| 7 | g5205.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 161 | 425 | 4.12E-60 |
| 6 | g5205.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 429 | 758 | 8.69E-74 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5205/g5205.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5205.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016817 | hydrolase activity, acting on acid anhydrides | MF |
| GO:0005524 | ATP binding | MF |
| GO:0070615 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K10875 (DNA repair and recombination protein RAD54 and RAD54-like protein [EC:5.6.2.-])
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.
