General information for g3238.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Fanconi anemia group M protein.
Parent gene
- The parent gene g3238 is located on chr_3: 23951306..23958947 (+ 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_3 | g3238 | g3238.t1 | TSS | g3238.t1 | 23951235 | 23951235 |
| chr_3 | g3238 | g3238.t1 | isoform | g3238.t1 | 23951306 | 23958947 |
| chr_3 | g3238 | g3238.t1 | exon | g3238.t1.exon1 | 23951306 | 23951424 |
| chr_3 | g3238 | g3238.t1 | cds | g3238.t1.CDS1 | 23951306 | 23951424 |
| chr_3 | g3238 | g3238.t1 | exon | g3238.t1.exon2 | 23954531 | 23954901 |
| chr_3 | g3238 | g3238.t1 | cds | g3238.t1.CDS2 | 23954531 | 23954901 |
| chr_3 | g3238 | g3238.t1 | exon | g3238.t1.exon3 | 23954970 | 23956069 |
| chr_3 | g3238 | g3238.t1 | cds | g3238.t1.CDS3 | 23954970 | 23956069 |
| chr_3 | g3238 | g3238.t1 | exon | g3238.t1.exon4 | 23956131 | 23958947 |
| chr_3 | g3238 | g3238.t1 | cds | g3238.t1.CDS4 | 23956131 | 23958947 |
| chr_3 | g3238 | g3238.t1 | TTS | g3238.t1 | NA | NA |
Sequences
>g3238.t1 Gene=g3238 Length=4407
ATGGCAACTGCTGTAATTTCTAGAGAACAAGCATCAGAAGATGAAGTACAACGTGAAATT
AATGAAGTCAATGCATTATTAGCGCAATATGATGAAGAAGAAGATGCTTCTTGGCTTGCT
GAATTAAACTTAAATAATTCAAATAATCAATCTGTATTAAATGCATCAAATGGACATCTA
GTAAATAATTCTGTTTGTGATGGTTTCGATGTAACAGCTGGTTCTACTTGGCTTTTTCCA
ACAAGTTATGAGAAAAGAGAATATCAGTTGAATATAAGTCGAAGTACTCTTTTTTATAAC
ACTCTTGTTATTCTTCCAACTGGACTTGGTAAAACTTTGATTGCATCTGTAACGATATAT
AATTTCTTTCGCTGGTTTCCTAAGTCGAAAATAATATTCATGGCGCCGACACGTCCACTC
GTAAATCAGCAAATTAGTGCATGCTATAAGGTTGTAGGAATTCCAAAAGAAGACACAGCT
GAATTAACTGGTAAAATTAACAAAGATAAGAGAAAAGAATATTGGAATACAAAAAGAGTA
TTTTTTGCTACACCTCAAGTTGTTCAAAGTGACTTAGCTCAAGGAATTTTACCTACAAAT
CTCATAAAATTACTTATTTTTGATGAAGCACATAAAGCAAAAGGAGAGTATGCATATTGC
AAAGTAATCAATGAAGTGCTCAAGGTTCAAAATAAATTTCGAGTTCTTGCTTTAACAGCA
ACTGCAGGCAAAACTAACAATGTGATAGATATCGTTAAAAATTTAATCATCTCAAAAATT
GAATATCGATCTGAACAATCTATAGATGTTCGAAGATACAGTCATCAAAAAGTTATAGAA
ACAATTGCCGTTAAAATTACTCCTGAGTTGAAACATATTAATGACTTCATTTTGGACTAC
GTTGATCCAATGATTCAAGAATTAAGGCAAGCAGGTTTTGTTAAAGCATACAATTTATCA
AAAGGATATTTAATAATGGAGCAGAATAAAATTAAGAGTAGTGATATGGAAATTGGTGAA
AAAAACACGCTTTTAAGACTAATCAACGAAGCCGTTAGTTTTTATCATTCTTTAGAAATT
CTTCAACGACACAGTGTTCATCTCTTTCTGAAATCATTAAAAGATGAAGTTACTAACAAA
TATAAATATTTTATAGTTAAGGATTTTAGGATTGTCCATTATATTAAAGAGTTAGAGAGA
AAATATGACAACCTAAATCCGTTAAAAATACCAGTTGAACAAATGTCTGCAGTTATGGAC
AAAGACATTGATTTTGGACATCCTAAATTTGATATTCTCAAGAATAAAACGGAAGAATAT
TTTAGAAATGGTGGATCTAAAGCAATCATCTTTTGCGAATATCGTGATACAACAGAGTTA
ATCTTTAAAGCACTGCTACAACTACGTCCACTCGTTAAACCAAAATGCCTCATTGGTCAA
GGGGGAAATATGTCTCAAAAAGAACAACTCAAAATTATGAAAGATTTTCGTGAAGCAGAT
ACAAATACATTGATTTGCACTTGTGTTGCTGAAGAAGGACTCGATATTGGTGAAGTCGAT
CTAGTCATTTGCTTTGATATTGGTTCAAAGAATTCTACACGTTTCGTTCAAAGAATTGGA
CGAACTGCTCGCAAAAGAAGTGGAAAAGTAATTGTGTTGGCAACGGAAGGTCGTGAATTA
GATATGATTAAAGAGTTAGTTGCCACAAAAGATTCAATGAACAAAAGTATTTCAAGAAGT
AAAGATATTTCCAAATACTTTTATACCTCTCCAAGACTTGTACCTAAAGAGTTTGAACCA
CAATGTATTGAAACCAAATTTGTAATTGGGTCAGAAAAAGTTGATGAAGAGGAAGGCAAA
AAAAAGAAAGGATCTACTAAGGGCAAGAAAGTTAAAGCATCATCTTCTAAAGAAAGCATA
ACAAATCACTTTAAACCAACTAGCAAAGGGAAGAAATCTGAAACAAAATCAGCTATTGTA
ATTTCTGAAGATGAAATTGAAGACAAGCAGCTTGATATTGATAAAGAATTAGATGAGGTA
ATGGAAGTTGAACCATGCATTGAAAGGGATGAAAAAAATCAAGATTATGGTCAATTGTAT
CTTGAGAAAGTTAATCAATTTATTAAAGACAATCAGCTAGAAGATAATAAATTTCTTCGT
GATCTTATTGATGATAGAGCGAGAGAAGGAGTTGATTCATTGAAACGATTAGCAAAAATG
CTTGAAAGTCCACCGAAAAAGGAAATTGTTGATATCAATTTCAATGATATCACTGACAAT
TTATGTTTATCACCCACACCAAAAAATAATTTAATTGAAATGGATGAAGAAATGAAGGAT
AATGAAAAAGAATTTGAATTGGTTGATTTTTGCCATGATAACTTTAATCGCTATGGAAAT
CAATTTAATGTCAGCAAAATGTCATCACCGTTTATTCCAGTGATTACAAAATTTAACGAA
TCAATCGAGCACCAACGACAAATAGAGAAGAATTTATTATTTGCTACTCCTGATTTTTCA
CAATTTCAACGACATCAAAGGAAAATTTCTGCATCAACACCATTGTGTGGTCGCAATTTG
ACTACAGCTATGCATGATATTTTTAAATTGCAAAATGATGATGAAGAGAGTCGTTTATCA
GATTTAGAATTAGACACTAAAGAAGACATGCAGAATATGCAACCGCAAACAGAAAAATTT
CCTTTTCTTGGAATCAATTCAATATCAGACATTTTTGAAGGTTGCGAGACAAATAACTTT
TCAAGTGCGTTTGTTCAAAAAAATTCCACCTCAAATCTAACTAGCAAATTGACGCAAATT
AAAAGTCGTAATTGGAAATCAGAAGACAAAAATGTTGAACATATAACTCAAAAATCAACT
GATGACAATAGCTTTGAAAAATCTCAAAATGACATACTTGAATTTTCAAATGATGATACA
CTCGTTCAAGTAATAAATAAATCCGATTCAAATAATACGTTATTCGAAACAGACTGTTAT
AAAAATGAAAAATCTATAGAAGATTCTATTGAAAAATTAAAAGACAAACTTAATGAATCA
TCAATAAGTAATAGTCATTGTTCAGTTGGGATTTCAAAAACAATTAATGATAAATCAGCA
TCAATTAGTGATCTCGAAAAAGAATTGATTAATTATGATACTCAAGACAAAGAAAATAGT
TTAGAAAAATATGATAATATCGAAGAGATTGATAAAAGCTTCACAAGTATTTCTGAAAGT
GAGCATTATGAAACTAAAGAGAAGGATGTTTTTGTAAAATTTAATTTGAATGATATAAAT
GATTTATTTGGAGAAGATGTTGAACTTTCATGCATATTACAAGATAAAAATATCCTAGAA
GAAAACATTAGTAGTTCTTCAGATAAAACAGTAGAATATGACTTTGAGTCAGAAATGACA
AAGATTGAAAATAATCCCAAATCATCATCATCAAATAAAAGTATTATGGAAGCTACAGAA
GAACCAATGGAAACTGAACAAGATGATTTCAAAGAAAATAATGAGTGTTCAACAAAATCA
ATCATACGTCCAAATATAACAAACTTTATGTCGGTAATCAAGAATAATTCTTTCGGAAAA
TCAGCGACTCAAAATGTACTAAAAACACAAAATCAGGGAAAAAATTGTGTTACACAAAAA
TTATTAGAAACAAATATAAAAAGAAGTGATACTGTCTTGTTAGATACTTCAATTAATAAA
ACTCCACCAATCAAAAGAACAAGGCCAATCGCTCTTCAAAATGATTCACCAGAGACACCT
ATTCGAAAGAGTAAAATTAAAAAACTAAACATTGAATTGAGTGATACTAGTGATACTGAT
TGCATCATACAAACTCCAATTTCTAAAAAGAATAAAAAGAAACGCAATGGTATAAATTCT
TTTTTCTTATCACAAGCAGATCATGATGATGATGATAGCAGTGAAGAAGATGATGGTGAC
CATGATTCAACAACTTTAAGAGATTTTGTTGTTGATACAACTATTCGAGAGACATTATCA
CGTACCAATATGCAATTACAATATCTTCAAAGCTTACGATCACCAAATGCACCAATCAAT
AGGAAAATTCTTTCACGACCTTTAAATCCTATGAATTTTAGTCAAATTTATTCACAAGCT
ATACAAGAAAGTGAATGTGAAGATGAAGAGAGTGACGATCTTGGATCTTTTATTGTAAAA
ACCGATGATGAAATTGAACAGGAAGAACTTTCAGAGATTGACGAGTTAGAGTTAGCTGAA
AAAGCATTGAAAAGAAAGCGACAATCTAAGAAGAATGAAAATGGAAATAAGAGTAAAACG
AGTAAAGTAAAGCGAGTAATTCGACCATTGGACAGTTCAAGTGAAGACGAGGATATGAGG
CAATTGAGAAGAGAGGTTGATATGTAA
>g3238.t1 Gene=g3238 Length=1468
MATAVISREQASEDEVQREINEVNALLAQYDEEEDASWLAELNLNNSNNQSVLNASNGHL
VNNSVCDGFDVTAGSTWLFPTSYEKREYQLNISRSTLFYNTLVILPTGLGKTLIASVTIY
NFFRWFPKSKIIFMAPTRPLVNQQISACYKVVGIPKEDTAELTGKINKDKRKEYWNTKRV
FFATPQVVQSDLAQGILPTNLIKLLIFDEAHKAKGEYAYCKVINEVLKVQNKFRVLALTA
TAGKTNNVIDIVKNLIISKIEYRSEQSIDVRRYSHQKVIETIAVKITPELKHINDFILDY
VDPMIQELRQAGFVKAYNLSKGYLIMEQNKIKSSDMEIGEKNTLLRLINEAVSFYHSLEI
LQRHSVHLFLKSLKDEVTNKYKYFIVKDFRIVHYIKELERKYDNLNPLKIPVEQMSAVMD
KDIDFGHPKFDILKNKTEEYFRNGGSKAIIFCEYRDTTELIFKALLQLRPLVKPKCLIGQ
GGNMSQKEQLKIMKDFREADTNTLICTCVAEEGLDIGEVDLVICFDIGSKNSTRFVQRIG
RTARKRSGKVIVLATEGRELDMIKELVATKDSMNKSISRSKDISKYFYTSPRLVPKEFEP
QCIETKFVIGSEKVDEEEGKKKKGSTKGKKVKASSSKESITNHFKPTSKGKKSETKSAIV
ISEDEIEDKQLDIDKELDEVMEVEPCIERDEKNQDYGQLYLEKVNQFIKDNQLEDNKFLR
DLIDDRAREGVDSLKRLAKMLESPPKKEIVDINFNDITDNLCLSPTPKNNLIEMDEEMKD
NEKEFELVDFCHDNFNRYGNQFNVSKMSSPFIPVITKFNESIEHQRQIEKNLLFATPDFS
QFQRHQRKISASTPLCGRNLTTAMHDIFKLQNDDEESRLSDLELDTKEDMQNMQPQTEKF
PFLGINSISDIFEGCETNNFSSAFVQKNSTSNLTSKLTQIKSRNWKSEDKNVEHITQKST
DDNSFEKSQNDILEFSNDDTLVQVINKSDSNNTLFETDCYKNEKSIEDSIEKLKDKLNES
SISNSHCSVGISKTINDKSASISDLEKELINYDTQDKENSLEKYDNIEEIDKSFTSISES
EHYETKEKDVFVKFNLNDINDLFGEDVELSCILQDKNILEENISSSSDKTVEYDFESEMT
KIENNPKSSSSNKSIMEATEEPMETEQDDFKENNECSTKSIIRPNITNFMSVIKNNSFGK
SATQNVLKTQNQGKNCVTQKLLETNIKRSDTVLLDTSINKTPPIKRTRPIALQNDSPETP
IRKSKIKKLNIELSDTSDTDCIIQTPISKKNKKKRNGINSFFLSQADHDDDDSSEEDDGD
HDSTTLRDFVVDTTIRETLSRTNMQLQYLQSLRSPNAPINRKILSRPLNPMNFSQIYSQA
IQESECEDEESDDLGSFIVKTDDEIEQEELSEIDELELAEKALKRKRQSKKNENGNKSKT
SKVKRVIRPLDSSSEDEDMRQLRREVDM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g3238.t1 | CDD | cd18033 | DEXDc_FANCM | 83 | 263 | 4.63435E-98 |
| 9 | g3238.t1 | Coils | Coil | Coil | 9 | 36 | - |
| 10 | g3238.t1 | Coils | Coil | Coil | 1406 | 1436 | - |
| 6 | g3238.t1 | Gene3D | G3DSA:3.40.50.300 | - | 80 | 274 | 1.9E-56 |
| 7 | g3238.t1 | Gene3D | G3DSA:3.40.50.300 | - | 284 | 559 | 4.3E-61 |
| 8 | g3238.t1 | Gene3D | G3DSA:1.20.1320.20 | hef helicase domain | 286 | 426 | 4.3E-61 |
| 16 | g3238.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 614 | 656 | - |
| 15 | g3238.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1142 | 1158 | - |
| 19 | g3238.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1142 | 1173 | - |
| 18 | g3238.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1304 | 1325 | - |
| 17 | g3238.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1424 | 1468 | - |
| 3 | g3238.t1 | PANTHER | PTHR14025:SF20 | FANCONI ANEMIA GROUP M PROTEIN | 47 | 1431 | 6.5E-194 |
| 4 | g3238.t1 | PANTHER | PTHR14025 | FANCONI ANEMIA GROUP M FANCM FAMILY MEMBER | 47 | 1431 | 6.5E-194 |
| 1 | g3238.t1 | Pfam | PF04851 | Type III restriction enzyme, res subunit | 88 | 242 | 2.9E-20 |
| 2 | g3238.t1 | Pfam | PF00271 | Helicase conserved C-terminal domain | 441 | 545 | 3.0E-21 |
| 21 | g3238.t1 | ProSiteProfiles | PS51192 | Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. | 92 | 260 | 19.638 |
| 20 | g3238.t1 | ProSiteProfiles | PS51194 | Superfamilies 1 and 2 helicase C-terminal domain profile. | 429 | 588 | 17.729 |
| 14 | g3238.t1 | SMART | SM00487 | ultradead3 | 81 | 271 | 3.1E-20 |
| 13 | g3238.t1 | SMART | SM00490 | helicmild6 | 456 | 546 | 1.1E-18 |
| 5 | g3238.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 129 | 561 | 1.76E-45 |
| 12 | g3238.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 98 | 120 | - |
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:0016787 | hydrolase activity | MF |
| GO:0006281 | DNA repair | BP |
| GO:0005524 | ATP binding | MF |
| GO:0043138 | 3’-5’ DNA helicase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10896 (fanconi anemia group M protein)
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.
