Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Gremlin-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_2 g5393 g5393.t1 TTS g5393.t1 9370775 9370775
chr_2 g5393 g5393.t1 isoform g5393.t1 9371251 9372045
chr_2 g5393 g5393.t1 exon g5393.t1.exon1 9371251 9372045
chr_2 g5393 g5393.t1 cds g5393.t1.CDS1 9371251 9372045
chr_2 g5393 g5393.t1 TSS g5393.t1 NA NA

Sequences

>g5393.t1 Gene=g5393 Length=795
ATGACGAGAGTGCATTTTGCAGCAATTTTTCTCTTCCTTCACATCATCGAATGTCATCGT
ATTCATTTATCAGACTCAATTATGGACATTATTAATACGCAGCATGTGGAAAAGATTTTA
GCTGATCGAAGGCAACAGCAAATGACGGCGGCAACAAGCAGCAATAATCTCGAAGAGGAG
GAGGATGCTGGCGCTGAAGAGACAGACACATATCCGACATCAGACACAATTATTGATTTT
GATTACAATACAAATCAGCCGCCACGTATTCGAGTTCCTTTGCCCATTCGTGGGGATGTT
GTTGTAAAATACAATGATACATCGATCATACCGTCATTACTGGCGACTCGTTATCCTAAC
GTCGATCCTAATCTTATCGACGATCTGCAAAAATATCGAGGCGATAAAATTCTAAAATCA
AGCAAAAGTGCACTATTTATTGCTAAGAAAGAACTACTGAAGCAAGATTGGTGCAAAACT
GAACCATTTGAGCAGAAAATTAGAGAAGATGGATGCTATTCTAAAAGAATTACCAACAAT
TTCTGCTATGGACAATGTAATTCATTCTATATTCCAAAGATGACGAGGCGACGACGAAAA
GTGCATGGAAAGCAACAACGTCAGCATCATAATAAACATCAGATTGATTCATTTCGATCA
TGTGCATATTGTAAGCCAAAAGAGTATAGCTTCATTGTCGTCATCCTCAAATGTCCTTCG
TTGACGCCAACATACCGACGAAAACGCGTGCAAGTTGTCAAGGAGTGCCGGTGCATCGCA
CAAAACGCAAACTAA

>g5393.t1 Gene=g5393 Length=264
MTRVHFAAIFLFLHIIECHRIHLSDSIMDIINTQHVEKILADRRQQQMTAATSSNNLEEE
EDAGAEETDTYPTSDTIIDFDYNTNQPPRIRVPLPIRGDVVVKYNDTSIIPSLLATRYPN
VDPNLIDDLQKYRGDKILKSSKSALFIAKKELLKQDWCKTEPFEQKIREDGCYSKRITNN
FCYGQCNSFYIPKMTRRRRKVHGKQQRQHHNKHQIDSFRSCAYCKPKEYSFIVVILKCPS
LTPTYRRKRVQVVKECRCIAQNAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5393.t1 Gene3D G3DSA:2.10.90.10 - 136 263 8.7E-36
13 g5393.t1 MobiDBLite mobidb-lite consensus disorder prediction 47 70 -
2 g5393.t1 PANTHER PTHR15283:SF4 GREMLIN 1 132 264 4.2E-54
3 g5393.t1 PANTHER PTHR15283 GREMLIN 1 132 264 4.2E-54
1 g5393.t1 Pfam PF03045 DAN domain 136 260 1.9E-36
8 g5393.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
9 g5393.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
10 g5393.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 13 -
11 g5393.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
7 g5393.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 264 -
12 g5393.t1 SMART SM00041 CT_3 160 264 9.5E-12
4 g5393.t1 SUPERFAMILY SSF57501 Cystine-knot cytokines 155 258 3.7E-5
5 g5393.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 18 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5393/g5393.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5393.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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. There were no conditions that were differentially expressed