Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein 60A.

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 g13568 g13568.t4 TTS g13568.t4 30959821 30959821
chr_1 g13568 g13568.t4 isoform g13568.t4 30960024 30961419
chr_1 g13568 g13568.t4 exon g13568.t4.exon1 30960024 30960149
chr_1 g13568 g13568.t4 cds g13568.t4.CDS1 30960024 30960149
chr_1 g13568 g13568.t4 exon g13568.t4.exon2 30960208 30960525
chr_1 g13568 g13568.t4 cds g13568.t4.CDS2 30960208 30960525
chr_1 g13568 g13568.t4 exon g13568.t4.exon3 30960775 30961024
chr_1 g13568 g13568.t4 cds g13568.t4.CDS3 30960775 30961024
chr_1 g13568 g13568.t4 exon g13568.t4.exon4 30961236 30961419
chr_1 g13568 g13568.t4 cds g13568.t4.CDS4 30961236 30961402
chr_1 g13568 g13568.t4 TSS g13568.t4 NA NA

Sequences

>g13568.t4 Gene=g13568 Length=878
ATCATCATGTTCCTGAAATGAGGCATACACATGGTAGAAGATTGTGGTTTGATATATCTG
AAATTGCTAATGATGTTTCACTATTGATGGCTGAATTGAGATTATATCAAAATTCTGTAT
TTAGCAAATATGAGGAAGAAAAGCAAGTTTGTGTGAGAGTTTATAAAGCTGATATAAGAA
ATGACCACGAAGACTTAAAACTGCTCTCATTTGTGAACACAACCACGCACACTGACGGTT
GGCTTGAGTTAAATGTTACACTCGCATTAAAAGAGTGGATTGAGCAAAGTGCAAGTAATA
TGGGATTTGTGATAAAAGCAAATTTAATTGAAAGACCAGATAAAGATTTAAGGCTTGATG
ATATTGGACTTGTCAGCTCACGTGGTGATGATGAATTTCAACCTTTTATGGTTGGATTTT
TCAAAGGACAAGAAATGATAAAACCGAAGAAAACAACAAAACATCATCACACAAGAACAA
AGAGACAAGCAAATCACAGAACTAAAAGCAAAAGAAAGTCAGATAATCGAAATCCATTTC
TATCGCCGGGTGAAAACAATCCAAAATCGTGCCAGATTAAAAATCTCTATGTGAGTTTCA
AGGACTTAAAATGGCAAGACTGGATCATTGCACCAGATGGATATGGAGCTTTTTATTGCG
ATGGCGAATGTAATTTTCCACTTAACGCCCATATGAACGCAAGTAATCATGCAATTGTTC
AAACACTAGTTCATCTAATGCATCCGACAAAGGTGCCAAAACCATGTTGTGCACCAACAA
AATTAAGTGCGATATCTGTTCTTTACTATCTTGATGATTCAAACGTAAATTTGAAAAAAT
ACAAAAATATGGTTGTAAAAAGTTGCGGATGCCATTAA

>g13568.t4 Gene=g13568 Length=286
MRHTHGRRLWFDISEIANDVSLLMAELRLYQNSVFSKYEEEKQVCVRVYKADIRNDHEDL
KLLSFVNTTTHTDGWLELNVTLALKEWIEQSASNMGFVIKANLIERPDKDLRLDDIGLVS
SRGDDEFQPFMVGFFKGQEMIKPKKTTKHHHTRTKRQANHRTKSKRKSDNRNPFLSPGEN
NPKSCQIKNLYVSFKDLKWQDWIIAPDGYGAFYCDGECNFPLNAHMNASNHAIVQTLVHL
MHPTKVPKPCCAPTKLSAISVLYYLDDSNVNLKKYKNMVVKSCGCH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13568.t4 CDD cd13761 TGF_beta_BMP5_like 184 286 1.75335E-73
7 g13568.t4 Gene3D G3DSA:2.60.120.970 - 1 132 1.1E-9
6 g13568.t4 Gene3D G3DSA:2.10.90.10 - 175 286 5.9E-44
11 g13568.t4 MobiDBLite mobidb-lite consensus disorder prediction 143 167 -
12 g13568.t4 MobiDBLite mobidb-lite consensus disorder prediction 143 179 -
3 g13568.t4 PANTHER PTHR11848:SF263 DAWDLE, ISOFORM A-RELATED 3 286 4.8E-91
4 g13568.t4 PANTHER PTHR11848 TGF-BETA FAMILY 3 286 4.8E-91
1 g13568.t4 Pfam PF00688 TGF-beta propeptide 2 134 1.8E-31
2 g13568.t4 Pfam PF00019 Transforming growth factor beta like domain 184 285 4.8E-36
9 g13568.t4 ProSitePatterns PS00250 TGF-beta family signature. 203 218 -
13 g13568.t4 ProSiteProfiles PS51362 TGF-beta family profile. 153 286 42.737
10 g13568.t4 SMART SM00204 TGFB_2 185 286 3.1E-65
5 g13568.t4 SUPERFAMILY SSF57501 Cystine-knot cytokines 179 285 1.38E-40

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:0008083 growth factor activity MF

KEGG

Orthology

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