General information for g1882.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g1882 is located on chr_3: 13641315..13642677 (+ strand)
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.t3 | isoform | g1882.t3 | 13636538 | 13642677 |
| chr_3 | g1882 | g1882.t3 | TSS | g1882.t3 | 13636538 | 13636538 |
| chr_3 | g1882 | g1882.t3 | exon | g1882.t3.exon1 | 13636538 | 13636624 |
| chr_3 | g1882 | g1882.t3 | exon | g1882.t3.exon2 | 13641269 | 13641381 |
| chr_3 | g1882 | g1882.t3 | cds | g1882.t3.CDS1 | 13641315 | 13641381 |
| chr_3 | g1882 | g1882.t3 | exon | g1882.t3.exon3 | 13641455 | 13641552 |
| chr_3 | g1882 | g1882.t3 | cds | g1882.t3.CDS2 | 13641455 | 13641552 |
| chr_3 | g1882 | g1882.t3 | exon | g1882.t3.exon4 | 13641612 | 13641746 |
| chr_3 | g1882 | g1882.t3 | cds | g1882.t3.CDS3 | 13641612 | 13641746 |
| chr_3 | g1882 | g1882.t3 | exon | g1882.t3.exon5 | 13641802 | 13641958 |
| chr_3 | g1882 | g1882.t3 | cds | g1882.t3.CDS4 | 13641802 | 13641958 |
| chr_3 | g1882 | g1882.t3 | exon | g1882.t3.exon6 | 13642223 | 13642677 |
| chr_3 | g1882 | g1882.t3 | cds | g1882.t3.CDS5 | 13642223 | 13642677 |
| chr_3 | g1882 | g1882.t3 | TTS | g1882.t3 | NA | NA |
Sequences
>g1882.t3 Gene=g1882 Length=1045
CAGTCGTTTCTCAACCGCGAGAGTGTGCAGATCGAAAAATCAAAATCTTTGCTTCTGCAC
GCACAACGTTTCATTAATACATTTTTTTTTGTGAGAATCTCTCCATGAATTTTCTATCAA
TACTCTAATAATTATGAATCACTCAGAAATATTATCATTTCTTCTACTACTATTTTGTGT
CTGTCAAAATTTCATTTCCGCATCACCACTTTTACCCTCCTCCTCATCATCAAATAATCG
TCGTCGAACGCGTTCGCAAATCGTAGCATGGAAACAGCCTGAAGATTATTGGAATATTAC
AAGCATTCCTAGAAGTATTTTACCTCATTTAATTAATAAAAATTTGAGCCATACGCTGCC
AGCACCAGCCAATATTATTTTTAAAACTGTCGATGCCGATGAAAAAATATTAGAGAGATT
TCATGAAATTAAGAATAATATCACTGCAAGAACATTGTGGTCAAAAGCAGAAGCTGATCA
TCATTACTCGCCATTTTTCGATAAAGCACTGAAACTTATGAATCTCCAACAAGTCGCTTT
TGAAATTGAAAACTCTGTGATGAGTAAAATGAGTTGTACAGCATGCAAAGCTGGAGCAAC
GCTACTTCAACATTATATAAAGTCTGGAAAGAGTAAAGAAGAAATCATTAAAACTATCTA
TCAATACTGCACAAACCTACAAATTCAATCAGCTAGAGTTTGTGAAGGTGTCAGCAATCT
CTTTGGTGGTGAAGTTATTTACGTTCTCAAAAGAACAAACTTGGGTGCAGATGAGATTTG
TAGTTTTATAATTGGTGATGCATGCGGAGACATTTATAATCCTTATCATGAATGGGAAAT
TGAATTGCCTCCTGTACCAAAGCCACAACCTCATGAACTACCAATACCAAAAGAAAATGC
ACCATCATTTAAAGTTCTTCATTTGAGTGACACACATTTTGACCCTTATTATGAGGAAGG
TAGTAATGCTGACTGTAATGAACCACTTTGCTGTAGAATAACTAATGGAAGACCAAGACA
TGTTAATGCGGCAGCTGGAAAGTAA
>g1882.t3 Gene=g1882 Length=303
MNHSEILSFLLLLFCVCQNFISASPLLPSSSSSNNRRRTRSQIVAWKQPEDYWNITSIPR
SILPHLINKNLSHTLPAPANIIFKTVDADEKILERFHEIKNNITARTLWSKAEADHHYSP
FFDKALKLMNLQQVAFEIENSVMSKMSCTACKAGATLLQHYIKSGKSKEEIIKTIYQYCT
NLQIQSARVCEGVSNLFGGEVIYVLKRTNLGADEICSFIIGDACGDIYNPYHEWEIELPP
VPKPQPHELPIPKENAPSFKVLHLSDTHFDPYYEEGSNADCNEPLCCRITNGRPRHVNAA
AGK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1882.t3 | Gene3D | G3DSA:1.10.225.10 | Saposin | 141 | 226 | 9.9E-8 |
| 2 | g1882.t3 | PANTHER | PTHR10340 | SPHINGOMYELIN PHOSPHODIESTERASE | 130 | 303 | 2.8E-47 |
| 3 | g1882.t3 | PANTHER | PTHR10340:SF34 | SPHINGOMYELIN PHOSPHODIESTERASE | 130 | 303 | 2.8E-47 |
| 1 | g1882.t3 | Pfam | PF05184 | Saposin-like type B, region 1 | 147 | 182 | 1.3E-6 |
| 10 | g1882.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 11 | g1882.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 12 | g1882.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 17 | - |
| 13 | g1882.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 23 | - |
| 9 | g1882.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 303 | - |
| 15 | g1882.t3 | ProSiteProfiles | PS50015 | Saposin B type domain profile. | 144 | 228 | 12.591 |
| 14 | g1882.t3 | SMART | SM00741 | sapb_4 | 146 | 224 | 6.4E-11 |
| 5 | g1882.t3 | SUPERFAMILY | SSF47862 | Saposin | 145 | 227 | 2.22E-12 |
| 4 | g1882.t3 | SUPERFAMILY | SSF56300 | Metallo-dependent phosphatases | 250 | 290 | 7.4E-5 |
| 7 | g1882.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 6 | g1882.t3 | 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.
