General information for g11583.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as DNA replication licensing factor MCM4.
Parent gene
- The parent gene g11583 is located on chr_1: 17323292..17326304 (+ 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 | g11583 | g11583.t1 | TSS | g11583.t1 | 17323179 | 17323179 |
| chr_1 | g11583 | g11583.t1 | isoform | g11583.t1 | 17323292 | 17326304 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon1 | 17323292 | 17323331 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS1 | 17323292 | 17323331 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon2 | 17323398 | 17324835 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS2 | 17323398 | 17324835 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon3 | 17324913 | 17325120 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS3 | 17324913 | 17325120 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon4 | 17325201 | 17325509 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS4 | 17325201 | 17325509 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon5 | 17325622 | 17325769 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS5 | 17325622 | 17325769 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon6 | 17325847 | 17326151 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS6 | 17325847 | 17326151 |
| chr_1 | g11583 | g11583.t1 | exon | g11583.t1.exon7 | 17326212 | 17326304 |
| chr_1 | g11583 | g11583.t1 | cds | g11583.t1.CDS7 | 17326212 | 17326304 |
| chr_1 | g11583 | g11583.t1 | TTS | g11583.t1 | 17326568 | 17326568 |
Sequences
>g11583.t1 Gene=g11583 Length=2541
ATGTCTGACGCTAACAAAACTCCAAGAAGAGAAAGCGATGATCAACAACCAATGTCATCA
GCAGCAACCGATACACCTATGAGAAATCCACCGTCGTCAGCATCAGGCCGTACGCCATTG
CATGAAGGATCCGATGCTTTTTCATTACCTCCATCTGCTACACCGAGATATATGAACGCA
TCTGAATTTGATTTAAATTCTCCTCTTAATTATGGTACACCTAGCTCTATTGGCTCAATT
AAAACTCCTCATTCTGGAATAGCAAATACTCCATTAAAAATGAGACCGGATATTCGTATT
GATAAACGAGTACGACAAGTTGCTGTTGGTCAACTCGAACCAATTACAGAAGTCGATTCT
CAATCAGAAAGCGGCACATCTAATACACAAGCTCAATTAATGGTTTGGGGTACAAATGTT
GTTATCAGTGAATGCAAGAACAAATTCAAATACTTTTTGCTTAGATATATTGATCCTGAA
GCCGAAAATGACGAGATTGAAGAAGGCATGAATCTCAATGAACCGCTATATTTACAAAAG
TTGGATGAAGTCAATTCACTAGAAGAACCATTTCTTAATGTTAATTGTGCACATTTAAAA
GCATTTGATGAACAACTTTATAATCAGTTAATTTGCTATCCTCAAGAAGTTATTCCTGCT
TTTGACATGGCTACCAATGAAGTTTTTTTTGAAAAATATCCCGCTGCTGTGTTGGAACAT
CAAATTCAAGTTCGCCCATTTAATGCCGAAAAGACTCGTAATATGAGAGCTTTGAATCCA
GAAGATATAGATCAATTAATTTCTATAAGCGGCATGGTGATTCGTTGTTCAAATATTATT
CCTGAGATGCGTGAAGCATTCTTTAAATGCATTGTATGTTCATTTACAACAACTGTTGAA
CTTGATAGAGGCCGCATTCAAGAACCAAATTTGTGTACACATTGTAACACAAATCATTGC
TTTCAATTAATTCATAATCGATCACATTTCACTGATAAGCAACTCGTCAAGCTTCAAGAA
TCACAAGAAGATATGGCTGCTGGTCAAACACCTCATAATATACTGATGTTTGCTTACAAC
GATTTAGTCGATAAAGTTCAACCGGGTGATCGTATTACAGTGACTGGAATCTATAGAGCG
ATACCAATTCAAGACAATCCTCGCCAACGCACAGTTTCGTCAGTATACAAAACACACATT
GATGTTGTTCACTTTCGTAAATTGGACAAAAAAAGATTATATGCTTCAGAAGAGGGAAAA
GAACATTTATTTTCACCGGAACGTATTGAGCTCATGCATACATTGGCAGAAAAACCTGAT
GTTTATGATAGATTGGCACGTACAATCGCTCCATCGATCTATGAAAATCTTGATATTAAA
AAGGGTATTCTGCTTCAACTCTTTGGTGGAACAAAGAAAAAACACTCTGCAGGTGGCCGT
CAAGGTTTTCGTTCTGAAATACATATTCTTTTGTGTGGCGATCCGGGTGTAAGCAAAAGT
CAATTGCTGCAATATGTTTTTAATCTTATTCCACGTTCACAATACACTTCTGGTAAAGGT
TCATCAGCGGTCGGTTTGACGGCCTATGTTACTCGTGATCCTGATACGCGTCAATTAACA
TTACAAACTGGCTCTCTTGTTCTAGCTGATAACGGTATTTGCTGTATAGACGAATTTGAT
AAAATGAGTGATGCAACTAGAAGTGTTTTACATGAAGTAATGGAACAATCAACCTTGAGC
ATTGCCAAAGCAGGAATAATTTGTCAACTTAATGCAAGAACATCAATTTTAGCTTCATGT
AATCCATCAGAATCACAATGGAACAAAAACAAAACAATTATTGAAAATGTCAATTTACCG
CACACTCTTATGAGTCGTTTCGATTTGATATTTTTAATATTGGATCCACAGGATGAACTT
TTTGATAAACGCTTGGCATCTCATTTAGTATCTCTTTACTATGCTGGTAAAATGGACGAT
GATGATGAATTATTTGATATGGGAGTATTAAGAGATTATATTGCATACGCACGTGAACAC
GTTCATCCAATATTGACAGACGAGGCGCAACAGAGACTTATACAAGCATATGTCGACATG
CGTAAAATTGGTTCGGGTCGTGGACAAATTTCTGCTTATCCACGTCAACTTGAAAGCTTG
ATTCGATTAGCAGAAGCGCATGCTAAAGTGCGACTAAGTCAAACTGTGGAAAACGTCGAT
GTCGAAGAAGCTTGGCGATTACATCGAGAAGCTTTGAAACAATCTGCAACTGATCCACTT
TCTGGAAAAATTGATATTGGTATTCTAACAACTGGTTTGTCTGCCACAGCACGAAAAAAG
CGAGCTGATTTGATTGCATTTATTAAGGATAATTTAAAGAAAAAGAATAAGGCCAAAACT
ATTCCATACCAAAAGCTCTTCACTGATATTAAGGAAGCATCTCCTATTCTTATAACACGT
GAACAATTTGAGGATGCCTTAAAAGAACTACAAGATGATGGAATTGTAAATGTTATGGGA
ACAACTATTCGTGTTTGTTAA
>g11583.t1 Gene=g11583 Length=846
MSDANKTPRRESDDQQPMSSAATDTPMRNPPSSASGRTPLHEGSDAFSLPPSATPRYMNA
SEFDLNSPLNYGTPSSIGSIKTPHSGIANTPLKMRPDIRIDKRVRQVAVGQLEPITEVDS
QSESGTSNTQAQLMVWGTNVVISECKNKFKYFLLRYIDPEAENDEIEEGMNLNEPLYLQK
LDEVNSLEEPFLNVNCAHLKAFDEQLYNQLICYPQEVIPAFDMATNEVFFEKYPAAVLEH
QIQVRPFNAEKTRNMRALNPEDIDQLISISGMVIRCSNIIPEMREAFFKCIVCSFTTTVE
LDRGRIQEPNLCTHCNTNHCFQLIHNRSHFTDKQLVKLQESQEDMAAGQTPHNILMFAYN
DLVDKVQPGDRITVTGIYRAIPIQDNPRQRTVSSVYKTHIDVVHFRKLDKKRLYASEEGK
EHLFSPERIELMHTLAEKPDVYDRLARTIAPSIYENLDIKKGILLQLFGGTKKKHSAGGR
QGFRSEIHILLCGDPGVSKSQLLQYVFNLIPRSQYTSGKGSSAVGLTAYVTRDPDTRQLT
LQTGSLVLADNGICCIDEFDKMSDATRSVLHEVMEQSTLSIAKAGIICQLNARTSILASC
NPSESQWNKNKTIIENVNLPHTLMSRFDLIFLILDPQDELFDKRLASHLVSLYYAGKMDD
DDELFDMGVLRDYIAYAREHVHPILTDEAQQRLIQAYVDMRKIGSGRGQISAYPRQLESL
IRLAEAHAKVRLSQTVENVDVEEAWRLHREALKQSATDPLSGKIDIGILTTGLSATARKK
RADLIAFIKDNLKKKNKAKTIPYQKLFTDIKEASPILITREQFEDALKELQDDGIVNVMG
TTIRVC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 23 | g11583.t1 | CDD | cd17755 | MCM4 | 444 | 751 | 0.0 |
| 21 | g11583.t1 | Gene3D | G3DSA:3.30.1640.10 | - | 140 | 249 | 6.1E-19 |
| 22 | g11583.t1 | Gene3D | G3DSA:2.40.50.140 | - | 255 | 391 | 1.0E-49 |
| 20 | g11583.t1 | Gene3D | G3DSA:2.20.28.10 | - | 282 | 331 | 1.0E-49 |
| 19 | g11583.t1 | Gene3D | G3DSA:3.40.50.300 | - | 425 | 758 | 3.2E-130 |
| 27 | g11583.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 44 | - |
| 26 | g11583.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 39 | - |
| 5 | g11583.t1 | PANTHER | PTHR11630:SF66 | DNA REPLICATION LICENSING FACTOR MCM4 | 119 | 841 | 0.0 |
| 6 | g11583.t1 | PANTHER | PTHR11630 | DNA REPLICATION LICENSING FACTOR MCM FAMILY MEMBER | 119 | 841 | 0.0 |
| 14 | g11583.t1 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 277 | 290 | 1.4E-28 |
| 12 | g11583.t1 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 325 | 337 | 1.4E-28 |
| 13 | g11583.t1 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 457 | 468 | 1.4E-28 |
| 7 | g11583.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 484 | 499 | 1.0E-27 |
| 9 | g11583.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 544 | 558 | 1.0E-27 |
| 11 | g11583.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 572 | 585 | 1.0E-27 |
| 8 | g11583.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 596 | 608 | 1.0E-27 |
| 16 | g11583.t1 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 605 | 622 | 1.4E-28 |
| 10 | g11583.t1 | PRINTS | PR01657 | Mini-chromosome maintenance (MCM) protein family signature | 623 | 631 | 1.0E-27 |
| 15 | g11583.t1 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 753 | 762 | 1.4E-28 |
| 4 | g11583.t1 | Pfam | PF14551 | MCM N-terminal domain | 146 | 248 | 3.0E-15 |
| 2 | g11583.t1 | Pfam | PF17207 | MCM OB domain | 255 | 381 | 5.6E-38 |
| 3 | g11583.t1 | Pfam | PF00493 | MCM P-loop domain | 430 | 652 | 2.0E-96 |
| 1 | g11583.t1 | Pfam | PF17855 | MCM AAA-lid domain | 669 | 751 | 5.5E-28 |
| 25 | g11583.t1 | ProSitePatterns | PS00847 | MCM family signature. | 552 | 560 | - |
| 28 | g11583.t1 | ProSiteProfiles | PS50051 | MCM family domain profile. | 441 | 649 | 88.52 |
| 24 | g11583.t1 | SMART | SM00350 | mcm | 251 | 753 | 1.7E-267 |
| 18 | g11583.t1 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 172 | 402 | 5.14E-66 |
| 17 | g11583.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 452 | 763 | 2.87E-40 |
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:0005524 | ATP binding | MF |
| GO:0042555 | MCM complex | CC |
| GO:0006260 | DNA replication | BP |
| GO:0006270 | DNA replication initiation | BP |
| GO:0032508 | DNA duplex unwinding | BP |
| GO:0003678 | DNA helicase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K02212 (DNA replication licensing factor MCM4)
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.
