Gene loci information

Transcript annotation

  • This transcript has been annotated as Structural maintenance of chromosomes protein 2.

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 g10517 g10517.t2 isoform g10517.t2 10315572 10316634
chr_1 g10517 g10517.t2 exon g10517.t2.exon1 10315572 10315573
chr_1 g10517 g10517.t2 exon g10517.t2.exon2 10315638 10316152
chr_1 g10517 g10517.t2 cds g10517.t2.CDS1 10315638 10316152
chr_1 g10517 g10517.t2 exon g10517.t2.exon3 10316216 10316476
chr_1 g10517 g10517.t2 cds g10517.t2.CDS2 10316216 10316476
chr_1 g10517 g10517.t2 exon g10517.t2.exon4 10316541 10316634
chr_1 g10517 g10517.t2 cds g10517.t2.CDS3 10316541 10316634
chr_1 g10517 g10517.t2 TSS g10517.t2 10316726 10316726
chr_1 g10517 g10517.t2 TTS g10517.t2 NA NA

Sequences

>g10517.t2 Gene=g10517 Length=872
ATGTATATTAAGTCTATAGTTATTGATGGATTTAAATCATATGGTAGAAGAACAGAAGTC
AACGGTTTTGATAGAGAATTTAACGCTATTACAGGTTTAAATGGGACGGGAAAGTCAAAC
ATATTGGATAGTATTTGCTTTGTATTGGGAATATCAAATCTTTCTCATGTGCGCGCCAAT
TCTCTTCAAGATCTTGTTTATAAATCTGGTCAAGCCGGTGTAACAAAAGCGACAGTAACA
ATTAATTTTGACAACACTAACAAAAATCAATGTCCTATTGGATTTGAAAATTGTAAAGAG
ATTTCTGTTGCCCGACAAATTGTTGTAGGCGGCAAGGGAAAATATCTAATCAATGGAAAA
AATGCACAGTATAAACAAATTCAAGATCTTTTCTGCTCTGTACAATTGAATGTGAATAAT
CCAAATTTCTTAATTATGCAAGGAAGAATTACAAAAGTACTGAACATGAAACCACCAGAA
ATTTTATCAATGATAGAAGAAGCTGCTGGAACAAGTATGTATGAAACAAAGCGTGAAAAA
TCAATGGCATTGATTCAAAAGAAAGATGCAAAGCTTGATGAACTCAACTCTTTAATCAGA
GATGATATTCAACCAAAGCTTGATAAATTACGCAAAGACCAACAACAATATGTTGAATAC
CAACGAATATGTCGCGACGTTGAATATCTTACAAGAATTCACATTTCATATAAATATATT
CAGTGTCGTAAGAATATTGAACAATGTGAAACAACAATCACTAATCTTAATGATGACATT
GAAAAAAATAAGGAAACTATTGTCAAAAATAATGACGAAATCAAAGAAATTGAGATTAAA
ATTCAAGAAATTCAAGAGCAACTCAATGCACA

>g10517.t2 Gene=g10517 Length=290
MYIKSIVIDGFKSYGRRTEVNGFDREFNAITGLNGTGKSNILDSICFVLGISNLSHVRAN
SLQDLVYKSGQAGVTKATVTINFDNTNKNQCPIGFENCKEISVARQIVVGGKGKYLINGK
NAQYKQIQDLFCSVQLNVNNPNFLIMQGRITKVLNMKPPEILSMIEEAAGTSMYETKREK
SMALIQKKDAKLDELNSLIRDDIQPKLDKLRKDQQQYVEYQRICRDVEYLTRIHISYKYI
QCRKNIEQCETTITNLNDDIEKNKETIVKNNDEIKEIEIKIQEIQEQLNA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g10517.t2 CDD cd03273 ABC_SMC2_euk 1 156 4.3074E-103
6 g10517.t2 Coils Coil Coil 246 290 -
5 g10517.t2 Gene3D G3DSA:3.40.50.300 - 1 184 8.0E-47
2 g10517.t2 PANTHER PTHR43977 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 1 287 1.2E-138
3 g10517.t2 PANTHER PTHR43977:SF2 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 1 287 1.2E-138
1 g10517.t2 Pfam PF02463 RecF/RecN/SMC N terminal domain 2 139 2.9E-36
4 g10517.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 287 7.97E-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:0005524 ATP binding MF
GO:0016887 ATP hydrolysis 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