Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g6855 g6855.t4 isoform g6855.t4 19195469 19196224
chr_2 g6855 g6855.t4 exon g6855.t4.exon1 19195469 19196224
chr_2 g6855 g6855.t4 cds g6855.t4.CDS1 19195529 19196056
chr_2 g6855 g6855.t4 TSS g6855.t4 NA NA
chr_2 g6855 g6855.t4 TTS g6855.t4 NA NA

Sequences

>g6855.t4 Gene=g6855 Length=756
GATATTTCACCGCAACTTAAAAGTAACAGTGCCAAAGTAAGACGTGCTAATAGTGCAAAA
GTTTCCACAACAACCAAATCAACAAAAAGCAGCTCAAAGCATTCAGCCAAATCAAAGCGT
TCACTAAGTCAACCGTCAGATTTAGATGTGATTGTGTGTGAAAGCAAAATGATGAGTAAT
TTGGACGATATTAAGCACATTGATGATGATGATGATGCATCGGATACAGATAGTCTTAGT
TCAAATCATGTAGATGAAATGGATGAAGAAGAAATTCAGAAAAATGCTGTAGTTTATGCT
GAAGTTCTCTATCAATTTAGAGCGGGTGGACCACAAGAATTATCGCTAGAGAAAGGAACA
TTAGTGGAGGTGATAAAACGTGAGACAGGCCCATGGTGGTGGGGACGAATAAAGTATGAT
GCTATTGTGAATGAAAGTGAACTTGAGATAAAGCAAGGATGGTTTCCTAAAGATTTTGTA
AAGGTGCTTCCCACATATGGAAATCGAAAATTTCTTCACCAACAATCATCAATCGACTGT
GATATCAATAATACAATTCTACCACCATCAACTGCCGCACCAAGCATCTCTTCTAGTCAA
TCAAATAGCGAAATAATGAGAGATAATGTCATCAAAGAATTGCTCGAGACAGAAATTAAT
TATGTTAAGTTACTTAATTCACTTGTCAATGGGTAAACACAAATATTATAATTGTTTGAA
TGATTTAATAAAATTTCTTTTCTTTCGTTCGTTAGA

>g6855.t4 Gene=g6855 Length=175
MMSNLDDIKHIDDDDDASDTDSLSSNHVDEMDEEEIQKNAVVYAEVLYQFRAGGPQELSL
EKGTLVEVIKRETGPWWWGRIKYDAIVNESELEIKQGWFPKDFVKVLPTYGNRKFLHQQS
SIDCDINNTILPPSTAAPSISSSQSNSEIMRDNVIKELLETEINYVKLLNSLVNG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g6855.t4 CDD cd00174 SH3 43 103 1.1735E-11
10 g6855.t4 Gene3D G3DSA:2.30.30.40 SH3 Domains 31 107 4.4E-17
11 g6855.t4 Gene3D G3DSA:1.20.900.10 - 128 175 1.7E-6
14 g6855.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 31 -
2 g6855.t4 PANTHER PTHR45834:SF3 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 3, ISOFORM L 21 175 1.8E-31
3 g6855.t4 PANTHER PTHR45834 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 9-RELATED 21 175 1.8E-31
7 g6855.t4 PRINTS PR00452 SH3 domain signature 42 52 5.1E-6
6 g6855.t4 PRINTS PR00452 SH3 domain signature 56 71 5.1E-6
4 g6855.t4 PRINTS PR00452 SH3 domain signature 73 82 5.1E-6
5 g6855.t4 PRINTS PR00452 SH3 domain signature 95 107 5.1E-6
1 g6855.t4 Pfam PF00018 SH3 domain 46 100 1.8E-6
16 g6855.t4 ProSiteProfiles PS50002 Src homology 3 (SH3) domain profile. 39 109 21.461
15 g6855.t4 ProSiteProfiles PS50010 Dbl homology (DH) domain profile. 150 175 8.633
13 g6855.t4 SMART SM00326 SH3_2 42 108 5.0E-11
9 g6855.t4 SUPERFAMILY SSF50044 SH3-domain 40 109 6.17E-15
8 g6855.t4 SUPERFAMILY SSF48065 DBL homology domain (DH-domain) 135 174 4.71E-7

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
GO:0005085 guanyl-nucleotide exchange factor 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