Gene loci information

Transcript annotation

  • This transcript has been annotated as Structural maintenance of chromosomes protein 4.

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_2 g6297 g6297.t2 isoform g6297.t2 16021289 16022510
chr_2 g6297 g6297.t2 exon g6297.t2.exon1 16021289 16021400
chr_2 g6297 g6297.t2 cds g6297.t2.CDS1 16021289 16021400
chr_2 g6297 g6297.t2 exon g6297.t2.exon2 16021531 16021682
chr_2 g6297 g6297.t2 cds g6297.t2.CDS2 16021531 16021682
chr_2 g6297 g6297.t2 exon g6297.t2.exon3 16021738 16022510
chr_2 g6297 g6297.t2 cds g6297.t2.CDS3 16021738 16022508
chr_2 g6297 g6297.t2 TSS g6297.t2 NA NA
chr_2 g6297 g6297.t2 TTS g6297.t2 NA NA

Sequences

>g6297.t2 Gene=g6297 Length=1037
ATGTCTAATAAAAATTCCAGGAAAAAATCACTTCCTGAACAGCAGCAACAGAAAATTGTT
GAAGATGAAGCTCCAATTGATGAAGATATGGATATTTCAGAAGATGAAGAAGGAGGAACT
AGAGTTGGTGGTATTTATATTCCTCCGCCAGTTAAACCATATTGTTCGACAGAAAGCAAA
GGACCACGTCTGGTTATTACTCATATTGAAAATACTAATTTTAAAAGTTATGCAAACACA
GTTAGTGTAGGACCATTTCATCATCGATTCTCTTCTGTAATTGGTCCAAATGGAAGTGGT
AAAAGTAATGTCATTGATTCAATGTTATTTGTTTTTGGCTATCGAGCTCAACAACTTCGA
TCAAAGAAAATGTCTGTTCTTATTCACAATTCTTCGAAATATTCAAACGTTAATAGCTGC
AAAGTAGCAGTCCATTTCAAACAAATTCTTGATAAAGAAGATGGCACATTTGAATTCATT
CCAAATAGTGAAATTGTTATTGCAAGAGTCGCTCATAAAAACAATACTTCATATTACACA
CTCAATGGACGCGAAGTGAAATTTAAAGAAGTAGCAAAAGTTCTTGAAGCACATGGAATT
GACTTACTTCATAATCGTTTCTTAATTTTGCAAGGAGAAGTTGAATCTATTGCATTGATG
AAAGCAAAAGCACAGGCACCAAATGAGACAGGTTTGCTTGAATATCTTGAAGATATCATT
GGAACTGAGCGATACAAAAAACCACTTACACTTATTAATGAACGATTGGAAAAACTTAAT
GAAGAGAGAACTGAAAAGCATAATCGATGTCGTCTAGCAGAACGTGAAATGAAAGATTTA
GAGTTACCAATGACTCAAGCTGTCGAATATTTGAAAATCGAAAATAAGCTGTATCAGGCT
CAAAGTTTACATCTACAATTATATGTTTATCATAAGAAGATTCAGATTGCAAAACACGAA
GAGGAAAAAGCTGAAGCAGCACAAAATTTGAAAGATCACGATGATAAATATAATGAAATT
AAGAATCAGCGGATAGA

>g6297.t2 Gene=g6297 Length=345
MSNKNSRKKSLPEQQQQKIVEDEAPIDEDMDISEDEEGGTRVGGIYIPPPVKPYCSTESK
GPRLVITHIENTNFKSYANTVSVGPFHHRFSSVIGPNGSGKSNVIDSMLFVFGYRAQQLR
SKKMSVLIHNSSKYSNVNSCKVAVHFKQILDKEDGTFEFIPNSEIVIARVAHKNNTSYYT
LNGREVKFKEVAKVLEAHGIDLLHNRFLILQGEVESIALMKAKAQAPNETGLLEYLEDII
GTERYKKPLTLINERLEKLNEERTEKHNRCRLAEREMKDLELPMTQAVEYLKIENKLYQA
QSLHLQLYVYHKKIQIAKHEEEKAEAAQNLKDHDDKYNEIKNQRI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6297.t2 Coils Coil Coil 249 276 -
8 g6297.t2 Coils Coil Coil 316 343 -
7 g6297.t2 Gene3D G3DSA:3.40.50.300 - 65 250 3.2E-41
6 g6297.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 41 -
5 g6297.t2 MobiDBLite mobidb-lite consensus disorder prediction 325 345 -
2 g6297.t2 PANTHER PTHR43939 - 60 341 2.3E-67
3 g6297.t2 PANTHER PTHR43939:SF1 STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 4 60 341 2.3E-67
1 g6297.t2 Pfam PF02463 RecF/RecN/SMC N terminal domain 66 201 3.3E-38
4 g6297.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 66 327 4.46E-34

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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