General information for g11583.t6
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.t6 | TSS | g11583.t6 | 17323179 | 17323179 |
| chr_1 | g11583 | g11583.t6 | isoform | g11583.t6 | 17323292 | 17324834 |
| chr_1 | g11583 | g11583.t6 | exon | g11583.t6.exon1 | 17323292 | 17323331 |
| chr_1 | g11583 | g11583.t6 | cds | g11583.t6.CDS1 | 17323292 | 17323331 |
| chr_1 | g11583 | g11583.t6 | exon | g11583.t6.exon2 | 17323398 | 17324834 |
| chr_1 | g11583 | g11583.t6 | cds | g11583.t6.CDS2 | 17323398 | 17324833 |
| chr_1 | g11583 | g11583.t6 | TTS | g11583.t6 | NA | NA |
Sequences
>g11583.t6 Gene=g11583 Length=1477
ATGTCTGACGCTAACAAAACTCCAAGAAGAGAAAGCGATGATCAACAACCAATGTCATCA
GCAGCAACCGATACACCTATGAGAAATCCACCGTCGTCAGCATCAGGCCGTACGCCATTG
CATGAAGGATCCGATGCTTTTTCATTACCTCCATCTGCTACACCGAGATATATGAACGCA
TCTGAATTTGATTTAAATTCTCCTCTTAATTATGGTACACCTAGCTCTATTGGCTCAATT
AAAACTCCTCATTCTGGAATAGCAAATACTCCATTAAAAATGAGACCGGATATTCGTATT
GATAAACGAGTACGACAAGTTGCTGTTGGTCAACTCGAACCAATTACAGAAGTCGATTCT
CAATCAGAAAGCGGCACATCTAATACACAAGCTCAATTAATGGTTTGGGGTACAAATGTT
GTTATCAGTGAATGCAAGAACAAATTCAAATACTTTTTGCTTAGATATATTGATCCTGAA
GCCGAAAATGACGAGATTGAAGAAGGCATGAATCTCAATGAACCGCTATATTTACAAAAG
TTGGATGAAGTCAATTCACTAGAAGAACCATTTCTTAATGTTAATTGTGCACATTTAAAA
GCATTTGATGAACAACTTTATAATCAGTTAATTTGCTATCCTCAAGAAGTTATTCCTGCT
TTTGACATGGCTACCAATGAAGTTTTTTTTGAAAAATATCCCGCTGCTGTGTTGGAACAT
CAAATTCAAGTTCGCCCATTTAATGCCGAAAAGACTCGTAATATGAGAGCTTTGAATCCA
GAAGATATAGATCAATTAATTTCTATAAGCGGCATGGTGATTCGTTGTTCAAATATTATT
CCTGAGATGCGTGAAGCATTCTTTAAATGCATTGTATGTTCATTTACAACAACTGTTGAA
CTTGATAGAGGCCGCATTCAAGAACCAAATTTGTGTACACATTGTAACACAAATCATTGC
TTTCAATTAATTCATAATCGATCACATTTCACTGATAAGCAACTCGTCAAGCTTCAAGAA
TCACAAGAAGATATGGCTGCTGGTCAAACACCTCATAATATACTGATGTTTGCTTACAAC
GATTTAGTCGATAAAGTTCAACCGGGTGATCGTATTACAGTGACTGGAATCTATAGAGCG
ATACCAATTCAAGACAATCCTCGCCAACGCACAGTTTCGTCAGTATACAAAACACACATT
GATGTTGTTCACTTTCGTAAATTGGACAAAAAAAGATTATATGCTTCAGAAGAGGGAAAA
GAACATTTATTTTCACCGGAACGTATTGAGCTCATGCATACATTGGCAGAAAAACCTGAT
GTTTATGATAGATTGGCACGTACAATCGCTCCATCGATCTATGAAAATCTTGATATTAAA
AAGGGTATTCTGCTTCAACTCTTTGGTGGAACAAAGAAAAAACACTCTGCAGGTGGCCGT
CAAGGTTTTCGTTCTGAAATACATATTCTTTTGTGTG
>g11583.t6 Gene=g11583 Length=492
MSDANKTPRRESDDQQPMSSAATDTPMRNPPSSASGRTPLHEGSDAFSLPPSATPRYMNA
SEFDLNSPLNYGTPSSIGSIKTPHSGIANTPLKMRPDIRIDKRVRQVAVGQLEPITEVDS
QSESGTSNTQAQLMVWGTNVVISECKNKFKYFLLRYIDPEAENDEIEEGMNLNEPLYLQK
LDEVNSLEEPFLNVNCAHLKAFDEQLYNQLICYPQEVIPAFDMATNEVFFEKYPAAVLEH
QIQVRPFNAEKTRNMRALNPEDIDQLISISGMVIRCSNIIPEMREAFFKCIVCSFTTTVE
LDRGRIQEPNLCTHCNTNHCFQLIHNRSHFTDKQLVKLQESQEDMAAGQTPHNILMFAYN
DLVDKVQPGDRITVTGIYRAIPIQDNPRQRTVSSVYKTHIDVVHFRKLDKKRLYASEEGK
EHLFSPERIELMHTLAEKPDVYDRLARTIAPSIYENLDIKKGILLQLFGGTKKKHSAGGR
QGFRSEIHILLC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11583.t6 | Gene3D | G3DSA:3.30.1640.10 | - | 140 | 249 | 2.6E-19 |
| 13 | g11583.t6 | Gene3D | G3DSA:2.40.50.140 | - | 255 | 391 | 4.2E-50 |
| 11 | g11583.t6 | Gene3D | G3DSA:2.20.28.10 | - | 282 | 331 | 4.2E-50 |
| 10 | g11583.t6 | Gene3D | G3DSA:3.40.50.300 | - | 425 | 492 | 9.9E-14 |
| 16 | g11583.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 44 | - |
| 15 | g11583.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 39 | - |
| 4 | g11583.t6 | PANTHER | PTHR11630:SF66 | DNA REPLICATION LICENSING FACTOR MCM4 | 118 | 492 | 8.8E-149 |
| 5 | g11583.t6 | PANTHER | PTHR11630 | DNA REPLICATION LICENSING FACTOR MCM FAMILY MEMBER | 118 | 492 | 8.8E-149 |
| 8 | g11583.t6 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 277 | 290 | 1.0E-14 |
| 6 | g11583.t6 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 325 | 337 | 1.0E-14 |
| 7 | g11583.t6 | PRINTS | PR01660 | Mini-chromosome maintenance (MCM) protein 4 signature | 457 | 468 | 1.0E-14 |
| 3 | g11583.t6 | Pfam | PF14551 | MCM N-terminal domain | 146 | 248 | 1.3E-15 |
| 1 | g11583.t6 | Pfam | PF17207 | MCM OB domain | 255 | 381 | 2.3E-38 |
| 2 | g11583.t6 | Pfam | PF00493 | MCM P-loop domain | 430 | 492 | 3.5E-13 |
| 17 | g11583.t6 | ProSiteProfiles | PS50051 | MCM family domain profile. | 441 | 492 | 17.442 |
| 14 | g11583.t6 | SMART | SM00350 | mcm | 251 | 492 | 3.1E-19 |
| 9 | g11583.t6 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins | 172 | 402 | 1.56E-66 |
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:0006270 | DNA replication initiation | BP |
| GO:0032508 | DNA duplex unwinding | BP |
| GO:0003678 | DNA helicase activity | MF |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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. There were no conditions that were differentially expressed