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.t4 TTS g3117.t4 22910835 22910835
chr_3 g3117 g3117.t4 isoform g3117.t4 22910840 22911961
chr_3 g3117 g3117.t4 exon g3117.t4.exon1 22910840 22911961
chr_3 g3117 g3117.t4 cds g3117.t4.CDS1 22910908 22911921
chr_3 g3117 g3117.t4 TSS g3117.t4 NA NA

Sequences

>g3117.t4 Gene=g3117 Length=1122
TAAACTAGAAAAACAAAATAAGAAAAAACTCGTTGATGAGATGGAAGAGGACACTGCAAA
AGCACGAAGAGATGTGGCATCATTAGCAAAAGATATTGCTACAATATCACATCAGATTTC
ATCTATTGAGAATAAAATTGACTCAAAGAGAAACGATCGTTTAAACATGTTGAGGCAGTG
TAAAATGGACGATATTCAAATACCCATGCTCGGTCATTCGAGCTTAGATGATATTTTAGC
AGAACAAGAAACAAATGACCCTTCATCATCAGCAACAATGTCAAACAGCATGTTATCAAA
AATCAATGAAATTCAACTTGATTACAGAAGTATTCCGAGAAATTTGAAAGATATTGATGA
ACCTGATCAAGTGAAAAAATCAGGTGATGGTTTGAATAAAGAACTTCAACAAAAACTAGA
TACTCTTGAGAAAATTCAAACGCCTAATATGAAAGCATTACAAAAACTTGATGCTGTTGC
AGAAAAGATTCAATCTACAAACGAAGAATTTGAAAATGCTAAGAAAAAGGCGAAGAAAGC
AAAAGCTGCATTTGAAAAAGTTAAAAATGAACGAATTGCTCGATTCAACAAGTGTCTAAA
TCACATTTCGGAAGCAATTGATGGTATTTACAAAGCACTCTCGCGCAATGATGCTGCACA
AGCTTTTCTTAATCCCGATAATCCAGAAGAATCTTATCTCGATGGTATCAACTATAATTG
CGTTGCACCAGGTAAACGTTTTCAACCGATGAGCAATCTTAGTGGTGGTGAAAAGACAAT
TGCAGCTTTAGCATTACTTTTTGCTATTCATAGCTATCAGCCTGCTCCGTTTTTTGTACT
TGATGAGATTGATGCCGCTCTTGATAATACTAACATTGGAAAAGTTGCAAAATATATTCG
TGAACAGCAAGATCTTCAGACAATTGTCATTTCATTAAAAGAAGAATTTTATGGTCATGC
TGATATTTTAATTGGTATTACACCACAACCTGCCGATTGTTTGGTCTCACGCACATACCT
TTATGATTTGACTAACTTTGAGAGTAACGATTAAATTTAAACTATTTTAATTTTATTAAC
ATGCTTTAAAAGAAAATAAATCTTAATAAATAAATGTAATTT

>g3117.t4 Gene=g3117 Length=337
MEEDTAKARRDVASLAKDIATISHQISSIENKIDSKRNDRLNMLRQCKMDDIQIPMLGHS
SLDDILAEQETNDPSSSATMSNSMLSKINEIQLDYRSIPRNLKDIDEPDQVKKSGDGLNK
ELQQKLDTLEKIQTPNMKALQKLDAVAEKIQSTNEEFENAKKKAKKAKAAFEKVKNERIA
RFNKCLNHISEAIDGIYKALSRNDAAQAFLNPDNPEESYLDGINYNCVAPGKRFQPMSNL
SGGEKTIAALALLFAIHSYQPAPFFVLDEIDAALDNTNIGKVAKYIREQQDLQTIVISLK
EEFYGHADILIGITPQPADCLVSRTYLYDLTNFESND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3117.t4 CDD cd03275 ABC_SMC1_euk 229 330 2.7978E-63
5 g3117.t4 Coils Coil Coil 136 177 -
4 g3117.t4 Gene3D G3DSA:3.40.50.300 - 53 335 5.3E-45
2 g3117.t4 PANTHER PTHR18937 STRUCTURAL MAINTENANCE OF CHROMOSOMES SMC FAMILY MEMBER 2 334 1.9E-122
1 g3117.t4 Pfam PF02463 RecF/RecN/SMC N terminal domain 101 316 1.8E-30
3 g3117.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 109 314 1.82E-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

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