Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative S-phase kinase-associated 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_2 g7517 g7517.t6 TSS g7517.t6 24201217 24201217
chr_2 g7517 g7517.t6 isoform g7517.t6 24201389 24202914
chr_2 g7517 g7517.t6 exon g7517.t6.exon1 24201389 24202340
chr_2 g7517 g7517.t6 cds g7517.t6.CDS1 24201419 24202340
chr_2 g7517 g7517.t6 exon g7517.t6.exon2 24202429 24202588
chr_2 g7517 g7517.t6 cds g7517.t6.CDS2 24202429 24202588
chr_2 g7517 g7517.t6 exon g7517.t6.exon3 24202725 24202914
chr_2 g7517 g7517.t6 cds g7517.t6.CDS3 24202725 24202914
chr_2 g7517 g7517.t6 TTS g7517.t6 24203031 24203031

Sequences

>g7517.t6 Gene=g7517 Length=1302
AGATACAAACGGCTTAAAGTTGACGAAAATATGTCCGAAAATTTTTCAAAATGCATCGAT
AGTGACGATAAGGATAGTAATTTATCTGTTACCATTTATGAAGACGAAAGTGATATAAGT
TATGTGCATAAATCGGCAAAGACTCGGTTAACAGTGGCTTCAAAGAGATCACCTTTAGTT
GCAATTAACAAACCATTAAATCAACATAACGTTCTGCAAGAATTCGCCAATAATCAAATT
CCATCTTCCTCAAAAACTCCTCTTAAACATAATGAAACTTTTCATCGCAAAATTTTACAA
AAAGAACCATCAATTGTCAGTTCATTTGATCTACTCTCTGATGAACTACTTCTTCACATC
TTCCAATATCTTCCGAAAAAAGCACTCAAACGACTTGCACAAGTGAATTCTAGATTTGCT
CGTGTTGTAGAAGACGAAACGCTATGGATTCGAATTGATCTCGCAAACAGATATATTACA
AAATATGCTTTTAGTCGTCTTCTTCCAAGAGGATTTATAATAATGAGACTGGCTCAAACC
AATATTGAAAGTCCTATTTTTAGCCCTCTTTTCAATGAAGATGGAAATTTTAAGTCAAAA
CTGCAATATTTAGATCTATCTCTGGCAAATGTTGATCTTAATTCATTAGCACAGCTATTA
GGAGTCTGCCGATCATTAAAAAAGTTAAGTCTGGAACAAGTGCCTCTCAATTTGGACGTA
TGTAAAGAAATATCTGAAAATCGAAATCTAGAAGTATTGAATCTTGCAATGTGCGAAGGA
ATAACGGACGATTGTGTATTAGTAATGATGAGCAACCTTCAATCACTCATAGCACTGAAT
ATTTCATGGACATCATTAACATCAGAGAGCATTGAAGCCATTGTTTCTCTCATTTCACCA
TCATTAATGCGTTTCAACATTTCTGGATGTCGACGAGGTTTTACTGATATAACACTCGAG
ACGCTTGTCAAACGTTGTCCCAATATCGTTGAGCTTGACGTTTCTGATTGTACGATGTTG
ACATCTGTTGCTATCGAAAATCTCTCGAAGCTTAATAAGCTTGAGTATCTGTCGCTGTCA
AGATGTTATAACATACCGATGACGTCTTACTTATCTCTCAATTCAATAAAATCCCTAATG
TTTTTGGATGTGTTCGGGCATATCTCCCCATCTGGAATTCAAATGCTTGAAAAGACTTTT
AAAAATATTGGGATCAATAAATTTATTCATAGCAGTGTTGCGCGTCCAACTGTAGCACCG
AGACGTACATCAATTTGGGGATTGAGAACTCGAGATATTTAG

>g7517.t6 Gene=g7517 Length=423
MSENFSKCIDSDDKDSNLSVTIYEDESDISYVHKSAKTRLTVASKRSPLVAINKPLNQHN
VLQEFANNQIPSSSKTPLKHNETFHRKILQKEPSIVSSFDLLSDELLLHIFQYLPKKALK
RLAQVNSRFARVVEDETLWIRIDLANRYITKYAFSRLLPRGFIIMRLAQTNIESPIFSPL
FNEDGNFKSKLQYLDLSLANVDLNSLAQLLGVCRSLKKLSLEQVPLNLDVCKEISENRNL
EVLNLAMCEGITDDCVLVMMSNLQSLIALNISWTSLTSESIEAIVSLISPSLMRFNISGC
RRGFTDITLETLVKRCPNIVELDVSDCTMLTSVAIENLSKLNKLEYLSLSRCYNIPMTSY
LSLNSIKSLMFLDVFGHISPSGIQMLEKTFKNIGINKFIHSSVARPTVAPRRTSIWGLRT
RDI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7517.t6 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 96 422 0.000000
3 g7517.t6 PANTHER PTHR16134:SF116 AT02038P-RELATED 92 412 0.000000
4 g7517.t6 PANTHER PTHR16134 F-BOX/TPR REPEAT PROTEIN POF3 92 412 0.000000
1 g7517.t6 Pfam PF12937 F-box-like 104 144 0.000000
2 g7517.t6 Pfam PF13516 Leucine Rich repeat 237 254 0.930000
14 g7517.t6 ProSiteProfiles PS50181 F-box domain profile. 96 142 11.697000
12 g7517.t6 SMART SM00256 fbox_2 102 142 0.000018
10 g7517.t6 SMART SM00367 LRR_CC_2 237 262 270.000000
9 g7517.t6 SMART SM00367 LRR_CC_2 263 287 330.000000
7 g7517.t6 SMART SM00367 LRR_CC_2 289 315 1.300000
11 g7517.t6 SMART SM00367 LRR_CC_2 316 341 0.001400
8 g7517.t6 SMART SM00367 LRR_CC_2 342 366 160.000000
6 g7517.t6 SUPERFAMILY SSF81383 F-box domain 96 180 0.000000
5 g7517.t6 SUPERFAMILY SSF52047 RNI-like 173 388 0.000000

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:0005515 protein binding MF

KEGG

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.

Raw TPM values