Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Smoothelin-like protein 1.

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_1 g12001 g12001.t8 TSS g12001.t8 20280976 20280976
chr_1 g12001 g12001.t8 isoform g12001.t8 20281670 20283585
chr_1 g12001 g12001.t8 exon g12001.t8.exon1 20281670 20281829
chr_1 g12001 g12001.t8 cds g12001.t8.CDS1 20281809 20281829
chr_1 g12001 g12001.t8 exon g12001.t8.exon2 20282498 20282543
chr_1 g12001 g12001.t8 cds g12001.t8.CDS2 20282498 20282543
chr_1 g12001 g12001.t8 exon g12001.t8.exon3 20282680 20282785
chr_1 g12001 g12001.t8 cds g12001.t8.CDS3 20282680 20282785
chr_1 g12001 g12001.t8 exon g12001.t8.exon4 20282843 20283585
chr_1 g12001 g12001.t8 cds g12001.t8.CDS4 20282843 20282966
chr_1 g12001 g12001.t8 TTS g12001.t8 20283580 20283580

Sequences

>g12001.t8 Gene=g12001 Length=1055
TTCACCATCACCTCGAACACCAACAACACCCACTACTCCCGGAGGTTCTAAGAAAAATGG
TCCACTTTTTTCCTTCACTGATCCAGCACTCGCTAAGCGAGCATCCACCGTCAAAGAACA
ATTATTACAATGGGCGCAGATGAAGACGAAAGAATATGAGAACGTCAATATAGAAAATTT
CAGTACAAGTTGGTCAGATGGATTAGCATTTGCCGCTCTTATACACCACTTTTTACCCGA
TGCATTTGATTATAGCAAATTAACACCTAAAGATAGAAGACATAATTTTACTTTGGCATT
CCGGATTGCAGAAGAAAAAGCCGGTATTTGTCCTTTGCTTGATGTTGACGATATGGTTAT
GTATAAAAAGCCAGATTGGAAATGTGTGTTTTGCTACGTCCAGTCAATATATCGAAGATT
TAAAGATGAAATATAAAAGCAAAGGAAGAATATTAAGCATCAAAAAGGCTTTTTAAATGG
AAAATTTCTTCTTATTCATCACATTGATTTTAAGATAAAAAAAAGTTTTTATGACAATAG
TCTTTATGTTGAAATTTAAATTTGAGCAAGTCAAATGTATCATAATTTTTGTTGATTTAT
TCAATTTTATTTTCTTTTAAATTGTGATGTATAGAACGTGTATTAATTTTGTAAATTTTA
ATTCATCTGACTTAATTTTTGATGATTTTTTCTCCTTTCTTTTTTACATTTTTGTCAATC
TGTGGTTGTTGATTTTCTTTGAATGAAAAAATAATTTTTTATTTTAAAAGAAGATAATTT
TGTTTGCAAACATAAAACTCTCAAAATGGTGCAGGTTTATTGTACTAACTTTTCTATAAC
TATTTTTTTAATAAAACACTCATAACAGCAATGCTGTAATCAAAAAATTATGTGAAACTA
ATCATTAGAGTTAATTAAAATATTTTTTGTAACTTGATAATCATGAAACCATTATGAAAT
TGTTGGAAAAAAAACTAAAACTATGAAACAAAAAAGCAATACAATTGTAAAAACTTTTTA
CTGATGACAATAAAAATATTTTATTGAATCAAATT

>g12001.t8 Gene=g12001 Length=98
MKTKEYENVNIENFSTSWSDGLAFAALIHHFLPDAFDYSKLTPKDRRHNFTLAFRIAEEK
AGICPLLDVDDMVMYKKPDWKCVFCYVQSIYRRFKDEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12001.t8 CDD cd00014 CH 2 94 0.000
6 g12001.t8 Gene3D G3DSA:1.10.418.10 - 1 97 0.000
2 g12001.t8 PANTHER PTHR23167 CALPONIN HOMOLOGY DOMAIN-CONTAINING PROTEIN DDB_G0272472-RELATED 1 92 0.000
3 g12001.t8 PANTHER PTHR23167:SF48 AGAP011397-PA 1 92 0.000
1 g12001.t8 Pfam PF00307 Calponin homology (CH) domain 3 95 0.000
7 g12001.t8 ProSiteProfiles PS50021 Calponin homology (CH) domain profile. 1 95 21.019
5 g12001.t8 SMART SM00033 ch_5 1 90 0.000
4 g12001.t8 SUPERFAMILY SSF47576 Calponin-homology domain, CH-domain 2 96 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:0005515 protein binding 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. There were no conditions that were differentially expressed