Gene loci information

Transcript annotation

  • This transcript has been annotated as Cdc42-like protein.

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 g2677 g2677.t6 isoform g2677.t6 19683127 19685789
chr_3 g2677 g2677.t6 exon g2677.t6.exon1 19683127 19683191
chr_3 g2677 g2677.t6 TSS g2677.t6 19683130 19683130
chr_3 g2677 g2677.t6 exon g2677.t6.exon2 19684333 19684707
chr_3 g2677 g2677.t6 cds g2677.t6.CDS1 19684530 19684707
chr_3 g2677 g2677.t6 exon g2677.t6.exon3 19684772 19684881
chr_3 g2677 g2677.t6 cds g2677.t6.CDS2 19684772 19684881
chr_3 g2677 g2677.t6 exon g2677.t6.exon4 19684943 19685140
chr_3 g2677 g2677.t6 cds g2677.t6.CDS3 19684943 19685140
chr_3 g2677 g2677.t6 exon g2677.t6.exon5 19685229 19685789
chr_3 g2677 g2677.t6 cds g2677.t6.CDS4 19685229 19685234
chr_3 g2677 g2677.t6 TTS g2677.t6 19685785 19685785

Sequences

>g2677.t6 Gene=g2677 Length=1309
CTGACACATATTTTTGGGAAAAAGCAACGAACAACACTTTAGAAAACATTTATAAATTTA
TATAGATGTTTAGTTTTTCTAATTTGTAAATTTTTTAAGAATTTCAATTTATGTATTAAT
TGAAGACAAAAAACATAAGTGCATAATTAATAAATTGTTAAAAAGGAAAAGAAAAGAGAT
ACCATCAACAGTTAAAAAATTCATCAATTTGAAAGCAAAAGAAACACCATATTAACATTA
CGAAGAGACTTCAAAGGCCAAAATGCAGACCATAAAATGTGTTGTTGTTGGTGATGGTGC
AGTCGGTAAAACTTGCCTTCTGATCTCATACACGACAAATAAATTTCCATCTGAATACGT
TCCAACTGTCTTTGACAACTATGCAGTGACAGTAATGATTGGAGGTGAACCTTACACGCT
AGGTCTTTTTGACACAGCTGGTCAGGAGGATTATGACCGATTGAGGCCATTGTCTTATCC
ACAAACAGATGTCTTTTTAGTATGCTTTTCAGTTGTCAGTCCCAGCTCCTTCGAAAATGT
TAAAGAAAAGTGGGTACCAGAAATCACTCATCATTGTCAAAAAACACCATTCTTGTTAGT
CGGCACTCAAATCGATTTACGCGATGAAAATGGTACATTAGAGAAGCTGGCAAAGAATAA
ACAGAAACCGATAACTTTGGAGCAGGGTGAAAAATTGGCAAAGGAATTGAAGGCTGTCAA
ATATGTAGAATGTTCAGCATTGACTCAGGGCTGAAGAATGTATTTGATGAAGCTATATTA
GCAGCATTGGAACCGCCAGAACCAGCAAAAAAGAAGAGATGCAAGATCTTGTAGAAAGGG
AAAGGCCTCAACAATCAAAAACCATTTCGTATCCTAAAATATTCGATATGAAAATTTATT
TTTCGGGAGCTCTTCGACAACTTTTTTTTCTAAAGAAAATAGAAACCAATCGCAGAAAGA
AAATTTAATATTTTTGTTTATTTTACTATCGTACGCAAGGCATTTATTAAAGAACAAATT
TTCTGACTGTCAGAGAATTGCATGTTTCTTCATTTTATTTTCTTTCTGTTTTATTCTAAT
ACAATATAATCAATATTCAAAAGTGAGCAGTATGCATAAATATACACATATTTTTCAATT
ACTTTAAAAGAAGAAGAAAGTTTTGTTTCCTATTCTGGAACTAATGGGAACTTTTTTCAT
GGATCCAGGCAAAAATTATCATACATTAAAAATATTGTTAGGAACTATATTAAAATATAA
TTGAAGAGAAATAATTTTTAAAAAACAAAGGAAAAAAGTGGCAACAAAA

>g2677.t6 Gene=g2677 Length=163
MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAG
QEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCQKTPFLLVGTQIDLR
DENGTLEKLAKNKQKPITLEQGEKLAKELKAVKYVECSALTQG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g2677.t6 CDD cd01874 Cdc42 3 162 0.000
10 g2677.t6 Gene3D G3DSA:3.40.50.300 - 1 163 0.000
2 g2677.t6 PANTHER PTHR24072:SF262 CDC42L PROTEIN 1 162 0.000
3 g2677.t6 PANTHER PTHR24072 RHO FAMILY GTPASE 1 162 0.000
8 g2677.t6 PRINTS PR00449 Transforming protein P21 ras signature 4 25 0.000
4 g2677.t6 PRINTS PR00449 Transforming protein P21 ras signature 27 43 0.000
6 g2677.t6 PRINTS PR00449 Transforming protein P21 ras signature 44 66 0.000
5 g2677.t6 PRINTS PR00449 Transforming protein P21 ras signature 106 119 0.000
7 g2677.t6 PRINTS PR00449 Transforming protein P21 ras signature 154 163 0.000
1 g2677.t6 Pfam PF00071 Ras family 5 162 0.000
16 g2677.t6 ProSiteProfiles PS51420 small GTPase Rho family profile. 1 163 25.753
12 g2677.t6 SMART SM00173 ras_sub_4 1 162 0.000
13 g2677.t6 SMART SM00175 rab_sub_5 4 162 0.000
14 g2677.t6 SMART SM00174 rho_sub_3 6 163 0.000
9 g2677.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 3 162 0.000
15 g2677.t6 TIGRFAM TIGR00231 small_GTP: small GTP-binding protein domain 1 157 0.000

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:0007264 small GTPase mediated signal transduction BP
GO:0005525 GTP binding MF
GO:0003924 GTPase 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.

Raw TPM values