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_3 g1882 g1882.t1 isoform g1882.t1 13641315 13642677
chr_3 g1882 g1882.t1 exon g1882.t1.exon1 13641315 13641381
chr_3 g1882 g1882.t1 cds g1882.t1.CDS1 13641315 13641381
chr_3 g1882 g1882.t1 exon g1882.t1.exon2 13641455 13641552
chr_3 g1882 g1882.t1 cds g1882.t1.CDS2 13641455 13641552
chr_3 g1882 g1882.t1 exon g1882.t1.exon3 13641612 13641746
chr_3 g1882 g1882.t1 cds g1882.t1.CDS3 13641612 13641746
chr_3 g1882 g1882.t1 exon g1882.t1.exon4 13641802 13641958
chr_3 g1882 g1882.t1 cds g1882.t1.CDS4 13641802 13641958
chr_3 g1882 g1882.t1 exon g1882.t1.exon5 13642223 13642677
chr_3 g1882 g1882.t1 cds g1882.t1.CDS5 13642223 13642677
chr_3 g1882 g1882.t1 TSS g1882.t1 NA NA
chr_3 g1882 g1882.t1 TTS g1882.t1 NA NA

Sequences

>g1882.t1 Gene=g1882 Length=912
ATGAATCACTCAGAAATATTATCATTTCTTCTACTACTATTTTGTGTCTGTCAAAATTTC
ATTTCCGCATCACCACTTTTACCCTCCTCCTCATCATCAAATAATCGTCGTCGAACGCGT
TCGCAAATCGTAGCATGGAAACAGCCTGAAGATTATTGGAATATTACAAGCATTCCTAGA
AGTATTTTACCTCATTTAATTAATAAAAATTTGAGCCATACGCTGCCAGCACCAGCCAAT
ATTATTTTTAAAACTGTCGATGCCGATGAAAAAATATTAGAGAGATTTCATGAAATTAAG
AATAATATCACTGCAAGAACATTGTGGTCAAAAGCAGAAGCTGATCATCATTACTCGCCA
TTTTTCGATAAAGCACTGAAACTTATGAATCTCCAACAAGTCGCTTTTGAAATTGAAAAC
TCTGTGATGAGTAAAATGAGTTGTACAGCATGCAAAGCTGGAGCAACGCTACTTCAACAT
TATATAAAGTCTGGAAAGAGTAAAGAAGAAATCATTAAAACTATCTATCAATACTGCACA
AACCTACAAATTCAATCAGCTAGAGTTTGTGAAGGTGTCAGCAATCTCTTTGGTGGTGAA
GTTATTTACGTTCTCAAAAGAACAAACTTGGGTGCAGATGAGATTTGTAGTTTTATAATT
GGTGATGCATGCGGAGACATTTATAATCCTTATCATGAATGGGAAATTGAATTGCCTCCT
GTACCAAAGCCACAACCTCATGAACTACCAATACCAAAAGAAAATGCACCATCATTTAAA
GTTCTTCATTTGAGTGACACACATTTTGACCCTTATTATGAGGAAGGTAGTAATGCTGAC
TGTAATGAACCACTTTGCTGTAGAATAACTAATGGAAGACCAAGACATGTTAATGCGGCA
GCTGGAAAGTAA

>g1882.t1 Gene=g1882 Length=303
MNHSEILSFLLLLFCVCQNFISASPLLPSSSSSNNRRRTRSQIVAWKQPEDYWNITSIPR
SILPHLINKNLSHTLPAPANIIFKTVDADEKILERFHEIKNNITARTLWSKAEADHHYSP
FFDKALKLMNLQQVAFEIENSVMSKMSCTACKAGATLLQHYIKSGKSKEEIIKTIYQYCT
NLQIQSARVCEGVSNLFGGEVIYVLKRTNLGADEICSFIIGDACGDIYNPYHEWEIELPP
VPKPQPHELPIPKENAPSFKVLHLSDTHFDPYYEEGSNADCNEPLCCRITNGRPRHVNAA
AGK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g1882.t1 Gene3D G3DSA:1.10.225.10 Saposin 141 226 9.9E-8
2 g1882.t1 PANTHER PTHR10340 SPHINGOMYELIN PHOSPHODIESTERASE 130 303 2.8E-47
3 g1882.t1 PANTHER PTHR10340:SF34 SPHINGOMYELIN PHOSPHODIESTERASE 130 303 2.8E-47
1 g1882.t1 Pfam PF05184 Saposin-like type B, region 1 147 182 1.3E-6
10 g1882.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 23 -
11 g1882.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
12 g1882.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
13 g1882.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 23 -
9 g1882.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 24 303 -
15 g1882.t1 ProSiteProfiles PS50015 Saposin B type domain profile. 144 228 12.591
14 g1882.t1 SMART SM00741 sapb_4 146 224 6.4E-11
5 g1882.t1 SUPERFAMILY SSF47862 Saposin 145 227 2.22E-12
4 g1882.t1 SUPERFAMILY SSF56300 Metallo-dependent phosphatases 250 290 7.4E-5
7 g1882.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 23 -
6 g1882.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 22 -

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:0006629 lipid metabolic process BP

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