Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA mismatch repair protein Msh2.

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 g11543 g11543.t5 isoform g11543.t5 16952785 16954445
chr_1 g11543 g11543.t5 exon g11543.t5.exon1 16952785 16952789
chr_1 g11543 g11543.t5 exon g11543.t5.exon2 16952858 16953457
chr_1 g11543 g11543.t5 cds g11543.t5.CDS1 16952902 16953457
chr_1 g11543 g11543.t5 exon g11543.t5.exon3 16953544 16953590
chr_1 g11543 g11543.t5 cds g11543.t5.CDS2 16953544 16953590
chr_1 g11543 g11543.t5 exon g11543.t5.exon4 16953645 16953840
chr_1 g11543 g11543.t5 cds g11543.t5.CDS3 16953645 16953840
chr_1 g11543 g11543.t5 exon g11543.t5.exon5 16954026 16954445
chr_1 g11543 g11543.t5 cds g11543.t5.CDS4 16954026 16954081
chr_1 g11543 g11543.t5 TTS g11543.t5 16954516 16954516
chr_1 g11543 g11543.t5 TSS g11543.t5 NA NA

Sequences

>g11543.t5 Gene=g11543 Length=1268
TCTAGTTCGTGCAAGTTTTGATGATGATTTAAATGAAATAAAGAAAAATATGAATGACAT
TGAAGCAAAAATGAACAAAGAAACAAAATCCTCTGCGAGTAAATTAGGATTGGAAGAAGG
AAGCACATTAAAACTAGATTATGTTTCACATCTATCTTTTTTTCTCAGAGCATCTCGCAA
AGAAGATCAAACTATCCGAAAAAACAAACAATTTGAAATTATTGATACAGCGCGAGGATA
TTTGCGATTCACAACAGCAAAACTTAAGGAACTTAATGTTGAATATAATTCACTAAAAGC
ATCCTATGAAGAGCACCAAAAGATGATTGTAGCTGAAATATGCAAAATTATTGTTGGATA
TTCCCTTCCTTTGACAAATTTAAATCATTGCATTGCGACACTCGATGTTTTTGTCAGTTT
TGCCCATGTTGTAGACAATTCGCCAGGCTCTTATGTTCGTCCTGAAATATTTTCCTCTGA
AGAGAAACGCATATTACAAATAGAAGAATTACGTCATCCATGTTTAGAGTGTCAAGATAT
CGATTTCATACCAAATGACGTTAATTTTATAGAAAATGAAAGTGAGCTTTTAATTATTAC
TGGAGCTAATACATGCGGAAAGTCGACTTACATACGTAGTATCGGAATTGCTGTTTTGCT
TGCACATATAGGAATGTTTGTTCCATGTACTAGCGCTAAAATTTCAATGTGTGATTCAAT
TCTTGCTAGAATCGGCGCAGCAGATGATATACAAAAAAATTTAAGTACTTTCGCTGTTGA
AATGTGTGAGACAGCTGCTATACTTAGAACAGCTACAAAAAATTCATTGATTATCATTGA
TGAATTAGTATTTTTAACATGTAATTTCTCATTTAGGTCTTGGTTTAGCTTGGTCAATTT
CTGAACATCTCGCAAAAAATATTAAATGCTTTACGTTATTTGCAACGCATTTTCACGAAA
TCACAACTCTCGAAAATCAATTGTCAAATGTCAAAAATTATCATCTTGCTTCTGAAGTTA
AAAACGACAAGTTGTTATTGTTATTCCAAGTTATTCGTGGTCCAGTATTAAAATCATACG
GTATTCATGTGGCAGATATTGCGCATTTACCAGAATCTGTAGTAGTAGCAGCTAAAAGTT
ATTTGAAGGAACTTGAGGCGAATGATGTTGATAAAGAAAATTCTGAGAAGTTATCAAAAA
TTGAACGTTTATTAAAAAATATTGAGACTGATAAAAATCTTGATATTGATTTATTATCAA
TTTTTTAA

>g11543.t5 Gene=g11543 Length=284
MNDIEAKMNKETKSSASKLGLEEGSTLKLDYVSHLSFFLRASRKEDQTIRKNKQFEIIDT
ARGYLRFTTAKLKELNVEYNSLKASYEEHQKMIVAEICKIIVGYSLPLTNLNHCIATLDV
FVSFAHVVDNSPGSYVRPEIFSSEEKRILQIEELRHPCLECQDIDFIPNDVNFIENESEL
LIITGANTCGKSTYIRSIGIAVLLAHIGMFVPCTSAKISMCDSILARIGAADDIQKNLST
FAVEMCETAAILRTATKNSLIIIDELVFLTCNFSFRSWFSLVNF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11543.t5 Coils Coil Coil 65 92 -
9 g11543.t5 Gene3D G3DSA:1.10.1420.10 - 1 69 1.2E-15
8 g11543.t5 Gene3D G3DSA:3.40.50.300 - 136 271 8.1E-55
3 g11543.t5 PANTHER PTHR11361 DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER 7 266 9.1E-77
4 g11543.t5 PANTHER PTHR11361:SF35 DNA MISMATCH REPAIR PROTEIN MSH2 7 266 9.1E-77
2 g11543.t5 Pfam PF05190 MutS family domain IV 2 83 1.2E-12
1 g11543.t5 Pfam PF00488 MutS domain V 181 266 4.8E-35
7 g11543.t5 SMART SM00534 mutATP5 178 284 2.5E-12
5 g11543.t5 SUPERFAMILY SSF48334 DNA repair protein MutS, domain III 2 128 1.2E-18
6 g11543.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 135 266 2.55E-29

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:0032300 mismatch repair complex CC
GO:0006298 mismatch repair BP
GO:0030983 mismatched DNA binding 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.

Raw TPM values