General information for g12531.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA replication licensing factor Mcm2.
Parent gene
- The parent gene g12531 is located on chr_1: 24273666..24274364 (- 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 | g12531 | g12531.t1 | TTS | g12531.t1 | 24271272 | 24271272 |
| chr_1 | g12531 | g12531.t1 | isoform | g12531.t1 | 24271421 | 24274364 |
| chr_1 | g12531 | g12531.t1 | exon | g12531.t1.exon1 | 24271421 | 24271945 |
| chr_1 | g12531 | g12531.t1 | cds | g12531.t1.CDS1 | 24271421 | 24271945 |
| chr_1 | g12531 | g12531.t1 | exon | g12531.t1.exon2 | 24272010 | 24272414 |
| chr_1 | g12531 | g12531.t1 | cds | g12531.t1.CDS2 | 24272010 | 24272414 |
| chr_1 | g12531 | g12531.t1 | exon | g12531.t1.exon3 | 24272487 | 24272692 |
| chr_1 | g12531 | g12531.t1 | cds | g12531.t1.CDS3 | 24272487 | 24272692 |
| chr_1 | g12531 | g12531.t1 | exon | g12531.t1.exon4 | 24272758 | 24274282 |
| chr_1 | g12531 | g12531.t1 | cds | g12531.t1.CDS4 | 24272758 | 24274282 |
| chr_1 | g12531 | g12531.t1 | exon | g12531.t1.exon5 | 24274350 | 24274364 |
| chr_1 | g12531 | g12531.t1 | cds | g12531.t1.CDS5 | 24274350 | 24274364 |
| chr_1 | g12531 | g12531.t1 | TSS | g12531.t1 | 24274469 | 24274469 |
Sequences
>g12531.t1 Gene=g12531 Length=2676
ATGTCTCAAAACGGAACACCACATGATGATGATTTGCGTTCACCGCCACCAACTCCATAT
TCGCCATCAACAGCAGCAGCAACACCAAGATCTAATCGTGAGCAATCACCTGTTGAAGAA
TTTGAGCCGTTTGAGAATGAAGCAGAATTGCTTGGTGAAATTGAAACAGCTGATGAAGAA
TCAGAGGGCGAAGATTTATTTGGAGGCGATATGGAAAGAGATTACCTTCCTAATCCAAGA
CTCGATAATTATGATCCTGAATTAGTGGACGATGATGAAAATTACAGTGTCATTAGTGAA
TCAGAGCGACGTGCTGCTGAAATGGAAATGAATAGACGAGATCGAGCAGCAGGCATTCAT
CGTGATGATCGAGATTTGATGTATGACAAAAGTGATGATGAAAGTGATATTCCGAGCTAT
AAACGTCGTCGTGCTGAGAAAGCAATTGAAGGCGTTGAAGAGGAAGAAATGATTGAATCA
ATTGAAAATCTTGAAGACACCAAAGGTCATACGATTAAAGAATGGGTATCAATGCTTGGT
CCTCGAACTGAAATTGCTAATCGATTTAAAAATTTCTTGAGAACATTTGTCGACGAGAAG
GGACAACAAACTTATCGTGATCGCATACGTAAAATGTGTGAACAAAATAAATCAAGCTTC
ATTGTAGTTTTCTCTGAGCTTGCTCATCATCAGCATGTTCTTGCTTATTTCTTGCCTGAA
GCACCTCAACAAATGTTGGAAATTTTCGATCAAGTTGCAAAAGAAATGGTTCTTTCAATT
TTTCCCACATATGAGAGAGTTACAAATGAAATTCATGTAAGAATTGCTGATTTACCATTG
ATTGAAGAATTGAGAACTTTTAGAAAACTGCATTTAAATCAATTGGTTCGCACTATGGGA
GTTGTTACAGCAACAACGGGAGTTTTACCTCAACTCTCTGTTGTTAAATACGATTGTGTG
AAATGTGGCTATATTATCGGACCATTTGTTCAAAATCAAAATGCTGAAGTAAAGCCTGGA
TCTTGTCCTGAATGTCAGAGTGCAGGACCTTTCTCAATAAACATGGAACAAACTCTCTAT
CGGAATTATCAAAAAATCACTTTACAAGAATCGCCTGGTCGCATTCCTGCTGGAAGAATT
CCGAGAAGCAAAGATTGCATTTTATTAGCTGATTTATGCGATCAATGTAAGCCAGGTGAT
GAAGTTGAAGTGACTGGAATTTATACAAACAATTATGATGGTTCATTAAATACTGATAAT
GGTTTCCCAGTATTTGCGACAGTGATCATAGCAAATCATATTTTAGTTAAAGACTCGAAG
CAAGTTGTTTCTTCTCTAACTGATGATGATGTTGCAACTATTCAACGTTTGAGTAAAGAA
CCAAGAATTGCTGAGAGAATTATAAGCAGTATTGCACCATCAATTTATGGACATGATTAT
ATTAAAAGAAGTTTGGCTCTTTCTCTCTTCGGAGGTGAAGCTAAAAATCCTGGCGAAAAA
CATAAATTGAGAGGTGACATTAATGTTCTTATTTGTGGAGATGCTGGTATGGCAAAATCT
CAATTTTTGAAATATGCTGAAAAGATTGCTCCTCGTGCTGTTTTCACAACTGGTCAAGGT
GCTAGTGCAGTAGGTCTGACAGCTTATGTTCGAAGAAATCCTATTTCCAAAGAATGGACA
CTTGAAGCGGGTGCATTAGTTTTGGCTGATCAAGGAGTTTGCTTAATTGATGAATTTGAT
AAAATGAATGATCAAGATCGTACATCAATTCATGAAGCTATGGAACAACAATCAATTAGT
ATTTCAAAAGCAGGCATTATAACATCTTTACAAGCTCGTTGTGCAGTTATTGCTGCATCA
AATCCTATTGGTGGTCGTTATGATCCGAGTTTGACGTTCTCTGAAAATGTGAATCTCTCG
GAACCAATTTTATCGCGTTTTGACATTTTGTGTGTTGTAAAAGATGAATTTGACCCTATG
CAAGATCAACGTTTAGCTGAATTTGTTGTTAAGTCACACATTCGTCATCATCCATCAAAC
GATGATCAGGAAAACGAAAATATGGAGGACATTAATGAGTTGGAATTACCACAAGATTTA
TTAAAGAAATATATTGTTTATGCGAAAGAGAACGTTAGACCCAAATTATCGAATATGGAC
CAAGATAAGATTGCAAAAATGTACTCACAATTGCGTCAAGAGTCGTTAGCAACAGGTTCT
TTACCTATCACTGTTCGTCACATTGAATCAGTAATTCGAATGGCTGAAGCACATGCTCGA
ATGCATTTGAGAGACACAGTTCAAGATGTTGATGTCAATATGGCAATTCGAATGATGCTT
GAAAGTTTCATTGCCGCTCAAAAGTTCTCGGTCATGAAAAAGATGCAGGTCACATTCCAA
AGATATTTGACATTCCAAAAAGATTATTCAGAGTTGCTCTTCTTCATTCTTCGTCAACTT
ACACTCGATCAACTTGCATACATTCGTTACAAGCAAGGACCATCAGCAACTCATGTCGAA
ATTTTGGAAAAAGATTTACTCGAACGTGCTAAACAAATTGATATTCACAATTTATCCAAA
TTTTATGAGAGTGAAATTTTCAAGAACAATGGTTTCTCATATGATAGCAAACGTAAGACA
ATTCTACAAGTTGTGCCTGAAGCAGCTACAGTTTAA
>g12531.t1 Gene=g12531 Length=891
MSQNGTPHDDDLRSPPPTPYSPSTAAATPRSNREQSPVEEFEPFENEAELLGEIETADEE
SEGEDLFGGDMERDYLPNPRLDNYDPELVDDDENYSVISESERRAAEMEMNRRDRAAGIH
RDDRDLMYDKSDDESDIPSYKRRRAEKAIEGVEEEEMIESIENLEDTKGHTIKEWVSMLG
PRTEIANRFKNFLRTFVDEKGQQTYRDRIRKMCEQNKSSFIVVFSELAHHQHVLAYFLPE
APQQMLEIFDQVAKEMVLSIFPTYERVTNEIHVRIADLPLIEELRTFRKLHLNQLVRTMG
VVTATTGVLPQLSVVKYDCVKCGYIIGPFVQNQNAEVKPGSCPECQSAGPFSINMEQTLY
RNYQKITLQESPGRIPAGRIPRSKDCILLADLCDQCKPGDEVEVTGIYTNNYDGSLNTDN
GFPVFATVIIANHILVKDSKQVVSSLTDDDVATIQRLSKEPRIAERIISSIAPSIYGHDY
IKRSLALSLFGGEAKNPGEKHKLRGDINVLICGDAGMAKSQFLKYAEKIAPRAVFTTGQG
ASAVGLTAYVRRNPISKEWTLEAGALVLADQGVCLIDEFDKMNDQDRTSIHEAMEQQSIS
ISKAGIITSLQARCAVIAASNPIGGRYDPSLTFSENVNLSEPILSRFDILCVVKDEFDPM
QDQRLAEFVVKSHIRHHPSNDDQENENMEDINELELPQDLLKKYIVYAKENVRPKLSNMD
QDKIAKMYSQLRQESLATGSLPITVRHIESVIRMAEAHARMHLRDTVQDVDVNMAIRMML
ESFIAAQKFSVMKKMQVTFQRYLTFQKDYSELLFFILRQLTLDQLAYIRYKQGPSATHVE
ILEKDLLERAKQIDIHNLSKFYESEIFKNNGFSYDSKRKTILQVVPEAATV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 24 | g12531.t1 | CDD | cd17753 | MCM2 | 466 | 782 | 0.0 |
| 22 | g12531.t1 | Gene3D | G3DSA:3.30.1640.10 | - | 181 | 280 | 3.5E-36 |
| 23 | g12531.t1 | Gene3D | G3DSA:2.40.50.140 | - | 289 | 434 | 4.6E-42 |
| 21 | g12531.t1 | Gene3D | G3DSA:2.20.28.10 | - | 311 | 361 | 4.6E-42 |
| 20 | g12531.t1 | Gene3D | G3DSA:3.40.50.300 | - | 447 | 787 | 1.3E-136 |
| 29 | g12531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 117 | - |
| 27 | g12531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 41 | 67 | - |
| 28 | g12531.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 96 | 117 | - |
| 6 | g12531.t1 | PANTHER | PTHR11630:SF44 | DNA REPLICATION LICENSING FACTOR MCM2 | 147 | 821 | 3.6E-295 |
| 7 | g12531.t1 | PANTHER | PTHR11630 | DNA REPLICATION LICENSING FACTOR MCM FAMILY MEMBER | 147 | 821 | 3.6E-295 |
| 9 | g12531.t1 | PRINTS | PR01658 | Mini-chromosome maintenance (MCM) protein 2 signature | 293 | 310 | 1.8E-30 |
| 8 | g12531.t1 | PRINTS | PR01658 | Mini-chromosome maintenance (MCM) protein 2 signature | 316 | 328 | 1.8E-30 |
| 10 | g12531.t1 | PRINTS | PR01658 | Mini-chromosome maintenance (MCM) protein 2 signature | 351 | 365 | 1.8E-30 |
| 12 | g12531.t1 | PRINTS | PR01658 | Mini-chromosome maintenance (MCM) protein 2 signature | 412 | 423 | 1.8E-30 |
| 11 | g12531.t1 | PRINTS | PR01658 | Mini-chromosome maintenance (MCM) protein 2 signature | 427 | 438 | 1.8E-30 |
| 17 | g12531.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 504 | 519 | 7.1E-30 |
| 15 | g12531.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 564 | 578 | 7.1E-30 |
| 14 | g12531.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 592 | 605 | 7.1E-30 |
| 16 | g12531.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 616 | 628 | 7.1E-30 |
| 13 | g12531.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 643 | 651 | 7.1E-30 |
| 3 | g12531.t1 | Pfam | PF12619 | Mini-chromosome maintenance protein 2 | 47 | 163 | 1.5E-15 |
| 5 | g12531.t1 | Pfam | PF14551 | MCM N-terminal domain | 187 | 275 | 6.7E-17 |
| 2 | g12531.t1 | Pfam | PF17207 | MCM OB domain | 284 | 410 | 1.4E-36 |
| 4 | g12531.t1 | Pfam | PF00493 | MCM P-loop domain | 451 | 673 | 4.5E-100 |
| 1 | g12531.t1 | Pfam | PF17855 | MCM AAA-lid domain | 699 | 783 | 1.1E-28 |
| 26 | g12531.t1 | ProSitePatterns | PS00847 | MCM family signature. | 572 | 580 | - |
| 30 | g12531.t1 | ProSiteProfiles | PS50051 | MCM family domain profile. | 463 | 669 | 91.189 |
| 25 | g12531.t1 | SMART | SM00350 | mcm | 280 | 784 | 0.0 |
| 19 | g12531.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 188 | 432 | 2.57E-64 |
| 18 | g12531.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 473 | 793 | 1.49E-37 |
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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006260 | DNA replication | BP |
| GO:0006270 | DNA replication initiation | BP |
| GO:0032508 | DNA duplex unwinding | BP |
| GO:0042555 | MCM complex | CC |
| GO:1905775 | negative regulation of DNA helicase activity | BP |
KEGG
Orthology
- This transcript has been annotated with K02540 (DNA replication licensing factor MCM2)
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.
