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.t1 TTS g13568.t1 30959821 30959821
chr_1 g13568 g13568.t1 isoform g13568.t1 30960024 30962254
chr_1 g13568 g13568.t1 exon g13568.t1.exon1 30960024 30960149
chr_1 g13568 g13568.t1 cds g13568.t1.CDS1 30960024 30960149
chr_1 g13568 g13568.t1 exon g13568.t1.exon2 30960208 30960525
chr_1 g13568 g13568.t1 cds g13568.t1.CDS2 30960208 30960525
chr_1 g13568 g13568.t1 exon g13568.t1.exon3 30960775 30961024
chr_1 g13568 g13568.t1 cds g13568.t1.CDS3 30960775 30961024
chr_1 g13568 g13568.t1 exon g13568.t1.exon4 30961236 30961419
chr_1 g13568 g13568.t1 cds g13568.t1.CDS4 30961236 30961419
chr_1 g13568 g13568.t1 exon g13568.t1.exon5 30961747 30961922
chr_1 g13568 g13568.t1 cds g13568.t1.CDS5 30961747 30961922
chr_1 g13568 g13568.t1 exon g13568.t1.exon6 30962028 30962254
chr_1 g13568 g13568.t1 cds g13568.t1.CDS6 30962028 30962254
chr_1 g13568 g13568.t1 TSS g13568.t1 30962679 30962679

Sequences

>g13568.t1 Gene=g13568 Length=1281
ATGGCACAAAATAATCTGCGAAATATTATACTTGTGAATTTTATGGTGCTTATTTTTATT
TATTGTGTTTATGCATCATATTCGGGTATTTATGTTGATGATGGACAACAGACAATATTA
CATCACCAATTAACGAGAGATGAAACGCATGAAGTGGAACATGAGATTCTGGAGTTATTG
GGACTGCCGGATAGACCGCGTAAGCGGCACATACATCCATCACTAAGAAAATCAGCGCCA
CAATTTCTACTAGATATTTATAAGAAATTAACATTGGAACAAGAAGATGACAATACAAGT
ACGAGAGTTAAACGCGATGCCAGTGACAATGAAATTTATTTAAGCGAAGCTGATCAATAT
GCAATCGATCAAGCTGATATTATCATGACTTTTCTTAATAAAAATCATCATGTTCCTGAA
ATGAGGCATACACATGGTAGAAGATTGTGGTTTGATATATCTGAAATTGCTAATGATGTT
TCACTATTGATGGCTGAATTGAGATTATATCAAAATTCTGTATTTAGCAAATATGAGGAA
GAAAAGCAAGTTTGTGTGAGAGTTTATAAAGCTGATATAAGAAATGACCACGAAGACTTA
AAACTGCTCTCATTTGTGAACACAACCACGCACACTGACGGTTGGCTTGAGTTAAATGTT
ACACTCGCATTAAAAGAGTGGATTGAGCAAAGTGCAAGTAATATGGGATTTGTGATAAAA
GCAAATTTAATTGAAAGACCAGATAAAGATTTAAGGCTTGATGATATTGGACTTGTCAGC
TCACGTGGTGATGATGAATTTCAACCTTTTATGGTTGGATTTTTCAAAGGACAAGAAATG
ATAAAACCGAAGAAAACAACAAAACATCATCACACAAGAACAAAGAGACAAGCAAATCAC
AGAACTAAAAGCAAAAGAAAGTCAGATAATCGAAATCCATTTCTATCGCCGGGTGAAAAC
AATCCAAAATCGTGCCAGATTAAAAATCTCTATGTGAGTTTCAAGGACTTAAAATGGCAA
GACTGGATCATTGCACCAGATGGATATGGAGCTTTTTATTGCGATGGCGAATGTAATTTT
CCACTTAACGCCCATATGAACGCAAGTAATCATGCAATTGTTCAAACACTAGTTCATCTA
ATGCATCCGACAAAGGTGCCAAAACCATGTTGTGCACCAACAAAATTAAGTGCGATATCT
GTTCTTTACTATCTTGATGATTCAAACGTAAATTTGAAAAAATACAAAAATATGGTTGTA
AAAAGTTGCGGATGCCATTAA

>g13568.t1 Gene=g13568 Length=426
MAQNNLRNIILVNFMVLIFIYCVYASYSGIYVDDGQQTILHHQLTRDETHEVEHEILELL
GLPDRPRKRHIHPSLRKSAPQFLLDIYKKLTLEQEDDNTSTRVKRDASDNEIYLSEADQY
AIDQADIIMTFLNKNHHVPEMRHTHGRRLWFDISEIANDVSLLMAELRLYQNSVFSKYEE
EKQVCVRVYKADIRNDHEDLKLLSFVNTTTHTDGWLELNVTLALKEWIEQSASNMGFVIK
ANLIERPDKDLRLDDIGLVSSRGDDEFQPFMVGFFKGQEMIKPKKTTKHHHTRTKRQANH
RTKSKRKSDNRNPFLSPGENNPKSCQIKNLYVSFKDLKWQDWIIAPDGYGAFYCDGECNF
PLNAHMNASNHAIVQTLVHLMHPTKVPKPCCAPTKLSAISVLYYLDDSNVNLKKYKNMVV
KSCGCH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13568.t1 CDD cd13761 TGF_beta_BMP5_like 324 426 2.31758E-72
7 g13568.t1 Gene3D G3DSA:2.60.120.970 - 42 272 2.3E-13
6 g13568.t1 Gene3D G3DSA:2.10.90.10 - 316 426 1.7E-43
15 g13568.t1 MobiDBLite mobidb-lite consensus disorder prediction 283 307 -
16 g13568.t1 MobiDBLite mobidb-lite consensus disorder prediction 283 319 -
3 g13568.t1 PANTHER PTHR11848:SF263 DAWDLE, ISOFORM A-RELATED 26 426 9.9E-105
4 g13568.t1 PANTHER PTHR11848 TGF-BETA FAMILY 26 426 9.9E-105
1 g13568.t1 Pfam PF00688 TGF-beta propeptide 36 274 1.5E-63
2 g13568.t1 Pfam PF00019 Transforming growth factor beta like domain 324 425 1.0E-35
8 g13568.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 8 -
10 g13568.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 9 27 -
9 g13568.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 28 426 -
14 g13568.t1 ProSitePatterns PS00250 TGF-beta family signature. 343 358 -
17 g13568.t1 ProSiteProfiles PS51362 TGF-beta family profile. 293 426 42.737
13 g13568.t1 SMART SM00204 TGFB_2 325 426 3.1E-65
5 g13568.t1 SUPERFAMILY SSF57501 Cystine-knot cytokines 319 425 3.87E-40
12 g13568.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 31 -

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