Gene loci information

Transcript annotation

  • This transcript has been annotated as Structural maintenance of chromosomes protein 1A.

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_3 g3117 g3117.t5 isoform g3117.t5 22913836 22914697
chr_3 g3117 g3117.t5 exon g3117.t5.exon1 22913836 22914526
chr_3 g3117 g3117.t5 cds g3117.t5.CDS1 22913838 22914526
chr_3 g3117 g3117.t5 exon g3117.t5.exon2 22914586 22914697
chr_3 g3117 g3117.t5 cds g3117.t5.CDS2 22914586 22914697
chr_3 g3117 g3117.t5 TSS g3117.t5 22914819 22914819
chr_3 g3117 g3117.t5 TTS g3117.t5 NA NA

Sequences

>g3117.t5 Gene=g3117 Length=803
ATGGCTGCGTTTTTGGAATTCATTGAAATCGAGAATTTCAAGAGTTATAAAGGAAAAGTT
GTTATTGGCCCATTGAAAAAATTTACTGCAGTTATTGGACCTAATGGAAGCGGTAAATCT
AATTTCATGGATGCAATATCTTTTGTAATGGGTGAAAAAACAACTTCCCTTCGTGTAAAG
AAACTTGGTGATTTGATTCATGGAGCTTCAATCTCTCGTCCTATATCAAGACATGCTTCA
GTTACAGCTAAATTTAAATTACCCGATGGAACTGATATGAGTTTCCAACGAGCTGTATCT
GGATCATCATCAGATTATAAAATTAACAATCAAAATGTTTCTAGCAACACATATTTATCT
GAACTCGAGAAAATGGGCATTAATGTAAAAGCAAAAAACTTTTTAGTGTTTCAAGGTGCT
GTTGAGAATATTGCTATGAAAAATGCAAAAGAACGCACACAATTATTTGAAGAAATCAGT
ACATCTGGATTATTGAAAGAAGAATACAACACTCTTAAACAAGAAATGATGAGTGCAGAA
GAAGAAACACAATTTACTTATCAGAAAAAGAAAGGTGTTGCTGCAGAGAGAAAGGAAGCA
AAATTGGAAAAACAAGAAGCTGATCGTTATTCACGTTTGCGAGAAGAATATACAGAGAAG
CAAATAATATATCAACTCTACAAGCTGTATCACAATGAAAAGGACATTCAAAGATACAAT
GACGAATTAAAATCAAAACAACAAGAATCAAAGAAGTTGGAAGATAAAAAGAGCCGTGCT
GATGAAGTATTACGAGATAAAAA

>g3117.t5 Gene=g3117 Length=267
MAAFLEFIEIENFKSYKGKVVIGPLKKFTAVIGPNGSGKSNFMDAISFVMGEKTTSLRVK
KLGDLIHGASISRPISRHASVTAKFKLPDGTDMSFQRAVSGSSSDYKINNQNVSSNTYLS
ELEKMGINVKAKNFLVFQGAVENIAMKNAKERTQLFEEISTSGLLKEEYNTLKQEMMSAE
EETQFTYQKKKGVAAERKEAKLEKQEADRYSRLREEYTEKQIIYQLYKLYHNEKDIQRYN
DELKSKQQESKKLEDKKSRADEVLRDK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g3117.t5 CDD cd03275 ABC_SMC1_euk 5 149 2.57756E-80
7 g3117.t5 Coils Coil Coil 162 182 -
8 g3117.t5 Coils Coil Coil 200 220 -
9 g3117.t5 Coils Coil Coil 229 266 -
6 g3117.t5 Gene3D G3DSA:3.40.50.300 - 2 175 2.4E-41
5 g3117.t5 MobiDBLite mobidb-lite consensus disorder prediction 242 267 -
2 g3117.t5 PANTHER PTHR18937:SF147 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 1B 3 265 1.1E-98
3 g3117.t5 PANTHER PTHR18937 STRUCTURAL MAINTENANCE OF CHROMOSOMES SMC FAMILY MEMBER 3 265 1.1E-98
1 g3117.t5 Pfam PF02463 RecF/RecN/SMC N terminal domain 5 130 8.8E-30
4 g3117.t5 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 5 260 6.12E-34

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:0007064 mitotic sister chromatid cohesion BP
GO:0016887 ATP hydrolysis activity MF
GO:0008278 cohesin complex CC

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. There were no conditions that were differentially expressed