Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA replication licensing factor Mcm2.

Parent gene

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.t7 TTS g12531.t7 24271272 24271272
chr_1 g12531 g12531.t7 isoform g12531.t7 24271421 24273666
chr_1 g12531 g12531.t7 exon g12531.t7.exon1 24271421 24271945
chr_1 g12531 g12531.t7 cds g12531.t7.CDS1 24271421 24271945
chr_1 g12531 g12531.t7 exon g12531.t7.exon2 24272010 24272414
chr_1 g12531 g12531.t7 cds g12531.t7.CDS2 24272010 24272414
chr_1 g12531 g12531.t7 exon g12531.t7.exon3 24272487 24272692
chr_1 g12531 g12531.t7 cds g12531.t7.CDS3 24272487 24272692
chr_1 g12531 g12531.t7 exon g12531.t7.exon4 24272758 24273666
chr_1 g12531 g12531.t7 cds g12531.t7.CDS4 24272758 24273664
chr_1 g12531 g12531.t7 TSS g12531.t7 24274469 24274469

Sequences

>g12531.t7 Gene=g12531 Length=2045
AAATGTGTGAACAAAATAAATCAAGCTTCATTGTAGTTTTCTCTGAGCTTGCTCATCATC
AGCATGTTCTTGCTTATTTCTTGCCTGAAGCACCTCAACAAATGTTGGAAATTTTCGATC
AAGTTGCAAAAGAAATGGTTCTTTCAATTTTTCCCACATATGAGAGAGTTACAAATGAAA
TTCATGTAAGAATTGCTGATTTACCATTGATTGAAGAATTGAGAACTTTTAGAAAACTGC
ATTTAAATCAATTGGTTCGCACTATGGGAGTTGTTACAGCAACAACGGGAGTTTTACCTC
AACTCTCTGTTGTTAAATACGATTGTGTGAAATGTGGCTATATTATCGGACCATTTGTTC
AAAATCAAAATGCTGAAGTAAAGCCTGGATCTTGTCCTGAATGTCAGAGTGCAGGACCTT
TCTCAATAAACATGGAACAAACTCTCTATCGGAATTATCAAAAAATCACTTTACAAGAAT
CGCCTGGTCGCATTCCTGCTGGAAGAATTCCGAGAAGCAAAGATTGCATTTTATTAGCTG
ATTTATGCGATCAATGTAAGCCAGGTGATGAAGTTGAAGTGACTGGAATTTATACAAACA
ATTATGATGGTTCATTAAATACTGATAATGGTTTCCCAGTATTTGCGACAGTGATCATAG
CAAATCATATTTTAGTTAAAGACTCGAAGCAAGTTGTTTCTTCTCTAACTGATGATGATG
TTGCAACTATTCAACGTTTGAGTAAAGAACCAAGAATTGCTGAGAGAATTATAAGCAGTA
TTGCACCATCAATTTATGGACATGATTATATTAAAAGAAGTTTGGCTCTTTCTCTCTTCG
GAGGTGAAGCTAAAAATCCTGGCGAAAAACATAAATTGAGAGGTGACATTAATGTTCTTA
TTTGTGGAGATGCTGGTATGGCAAAATCTCAATTTTTGAAATATGCTGAAAAGATTGCTC
CTCGTGCTGTTTTCACAACTGGTCAAGGTGCTAGTGCAGTAGGTCTGACAGCTTATGTTC
GAAGAAATCCTATTTCCAAAGAATGGACACTTGAAGCGGGTGCATTAGTTTTGGCTGATC
AAGGAGTTTGCTTAATTGATGAATTTGATAAAATGAATGATCAAGATCGTACATCAATTC
ATGAAGCTATGGAACAACAATCAATTAGTATTTCAAAAGCAGGCATTATAACATCTTTAC
AAGCTCGTTGTGCAGTTATTGCTGCATCAAATCCTATTGGTGGTCGTTATGATCCGAGTT
TGACGTTCTCTGAAAATGTGAATCTCTCGGAACCAATTTTATCGCGTTTTGACATTTTGT
GTGTTGTAAAAGATGAATTTGACCCTATGCAAGATCAACGTTTAGCTGAATTTGTTGTTA
AGTCACACATTCGTCATCATCCATCAAACGATGATCAGGAAAACGAAAATATGGAGGACA
TTAATGAGTTGGAATTACCACAAGATTTATTAAAGAAATATATTGTTTATGCGAAAGAGA
ACGTTAGACCCAAATTATCGAATATGGACCAAGATAAGATTGCAAAAATGTACTCACAAT
TGCGTCAAGAGTCGTTAGCAACAGGTTCTTTACCTATCACTGTTCGTCACATTGAATCAG
TAATTCGAATGGCTGAAGCACATGCTCGAATGCATTTGAGAGACACAGTTCAAGATGTTG
ATGTCAATATGGCAATTCGAATGATGCTTGAAAGTTTCATTGCCGCTCAAAAGTTCTCGG
TCATGAAAAAGATGCAGGTCACATTCCAAAGATATTTGACATTCCAAAAAGATTATTCAG
AGTTGCTCTTCTTCATTCTTCGTCAACTTACACTCGATCAACTTGCATACATTCGTTACA
AGCAAGGACCATCAGCAACTCATGTCGAAATTTTGGAAAAAGATTTACTCGAACGTGCTA
AACAAATTGATATTCACAATTTATCCAAATTTTATGAGAGTGAAATTTTCAAGAACAATG
GTTTCTCATATGATAGCAAACGTAAGACAATTCTACAAGTTGTGCCTGAAGCAGCTACAG
TTTAA

>g12531.t7 Gene=g12531 Length=680
MCEQNKSSFIVVFSELAHHQHVLAYFLPEAPQQMLEIFDQVAKEMVLSIFPTYERVTNEI
HVRIADLPLIEELRTFRKLHLNQLVRTMGVVTATTGVLPQLSVVKYDCVKCGYIIGPFVQ
NQNAEVKPGSCPECQSAGPFSINMEQTLYRNYQKITLQESPGRIPAGRIPRSKDCILLAD
LCDQCKPGDEVEVTGIYTNNYDGSLNTDNGFPVFATVIIANHILVKDSKQVVSSLTDDDV
ATIQRLSKEPRIAERIISSIAPSIYGHDYIKRSLALSLFGGEAKNPGEKHKLRGDINVLI
CGDAGMAKSQFLKYAEKIAPRAVFTTGQGASAVGLTAYVRRNPISKEWTLEAGALVLADQ
GVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIITSLQARCAVIAASNPIGGRYDPSL
TFSENVNLSEPILSRFDILCVVKDEFDPMQDQRLAEFVVKSHIRHHPSNDDQENENMEDI
NELELPQDLLKKYIVYAKENVRPKLSNMDQDKIAKMYSQLRQESLATGSLPITVRHIESV
IRMAEAHARMHLRDTVQDVDVNMAIRMMLESFIAAQKFSVMKKMQVTFQRYLTFQKDYSE
LLFFILRQLTLDQLAYIRYKQGPSATHVEILEKDLLERAKQIDIHNLSKFYESEIFKNNG
FSYDSKRKTILQVVPEAATV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g12531.t7 CDD cd17753 MCM2 255 571 0.0
21 g12531.t7 Gene3D G3DSA:3.30.1640.10 - 1 69 8.6E-22
22 g12531.t7 Gene3D G3DSA:2.40.50.140 - 78 223 3.0E-42
20 g12531.t7 Gene3D G3DSA:2.20.28.10 - 100 150 3.0E-42
19 g12531.t7 Gene3D G3DSA:3.40.50.300 - 236 576 6.8E-137
5 g12531.t7 PANTHER PTHR11630:SF44 DNA REPLICATION LICENSING FACTOR MCM2 1 610 2.3E-279
6 g12531.t7 PANTHER PTHR11630 DNA REPLICATION LICENSING FACTOR MCM FAMILY MEMBER 1 610 2.3E-279
11 g12531.t7 PRINTS PR01658 Mini-chromosome maintenance (MCM) protein 2 signature 82 99 5.1E-31
7 g12531.t7 PRINTS PR01658 Mini-chromosome maintenance (MCM) protein 2 signature 105 117 5.1E-31
9 g12531.t7 PRINTS PR01658 Mini-chromosome maintenance (MCM) protein 2 signature 140 154 5.1E-31
8 g12531.t7 PRINTS PR01658 Mini-chromosome maintenance (MCM) protein 2 signature 201 212 5.1E-31
10 g12531.t7 PRINTS PR01658 Mini-chromosome maintenance (MCM) protein 2 signature 216 227 5.1E-31
14 g12531.t7 PRINTS PR01657 Mini-chromosome maintenance (MCM) protein family signature 293 308 2.1E-30
16 g12531.t7 PRINTS PR01657 Mini-chromosome maintenance (MCM) protein family signature 353 367 2.1E-30
13 g12531.t7 PRINTS PR01657 Mini-chromosome maintenance (MCM) protein family signature 381 394 2.1E-30
15 g12531.t7 PRINTS PR01657 Mini-chromosome maintenance (MCM) protein family signature 405 417 2.1E-30
12 g12531.t7 PRINTS PR01657 Mini-chromosome maintenance (MCM) protein family signature 432 440 2.1E-30
4 g12531.t7 Pfam PF14551 MCM N-terminal domain 1 64 6.1E-7
2 g12531.t7 Pfam PF17207 MCM OB domain 73 199 9.6E-37
3 g12531.t7 Pfam PF00493 MCM P-loop domain 240 462 2.7E-100
1 g12531.t7 Pfam PF17855 MCM AAA-lid domain 488 572 7.3E-29
24 g12531.t7 ProSitePatterns PS00847 MCM family signature. 361 369 -
26 g12531.t7 ProSiteProfiles PS50051 MCM family domain profile. 252 458 91.189
25 g12531.t7 SMART SM00350 mcm 69 573 0.0
18 g12531.t7 SUPERFAMILY SSF50249 Nucleic acid-binding proteins 3 221 5.65E-57
17 g12531.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 262 582 7.58E-38

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

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.

Raw TPM values