Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Prosaposin.

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 g602 g602.t8 TSS g602.t8 4434335 4434335
chr_3 g602 g602.t8 isoform g602.t8 4434385 4435940
chr_3 g602 g602.t8 exon g602.t8.exon1 4434385 4434409
chr_3 g602 g602.t8 cds g602.t8.CDS1 4434385 4434409
chr_3 g602 g602.t8 exon g602.t8.exon2 4434520 4434598
chr_3 g602 g602.t8 cds g602.t8.CDS2 4434520 4434598
chr_3 g602 g602.t8 exon g602.t8.exon3 4434886 4435168
chr_3 g602 g602.t8 cds g602.t8.CDS3 4434886 4435168
chr_3 g602 g602.t8 exon g602.t8.exon4 4435272 4435940
chr_3 g602 g602.t8 cds g602.t8.CDS4 4435272 4435940
chr_3 g602 g602.t8 TTS g602.t8 NA NA

Sequences

>g602.t8 Gene=g602 Length=1056
ATGAAGATTTTGTTCTCAATTATTTCGTCTATTGTATCTAGTTCCGTTATATTGGGACGA
GAAAAATGCACATACGGGCCCTCATATTGGTGTAATAACTTAGTAAATGCAAAAAATTGC
GGAGCAGTTAAACACTGTATTAAAACAGTTTGGGAAAAACAACATGTACCGGAAGACACT
GATTCTATTTGCAAAATTTGTCTTGACATGGTAACCCAAGCCAGAGATCAACTCGAAAGC
AATGAAACTCAAGAAGAGTTGAAAGAAGTTTTCGATGGTTCTTGCGATTTGATACCGATA
AAAGTAGTAAAAACGGAATGCAAACGTTTGGCTGATGATTTCATACCAGAACTTGTTGAG
GCACTTGCTTCTCAAATGAATCCACAGGTCGTTTGTTCTACAGCTGGACTTTGTAATAAT
GCAAAGATTGATGCATTATTGGAAGAATATGAAATGCAGAAGAAAAATAATTTATTAAGT
TGCAACCAATGTAACAACATTGGAGAATTGATCACTCAAAAATTCCATACATCATCTCGT
GATCAAGTTCTAGATGGTTTCTTGAGTGCCTGCGGTCGTCTTTCATCGTTTTCTGATGCA
TGTTCTAGTATCATTCTGACTTATTTCAACGAAATCTATGAAGAACTTTCGAGAAATCTA
AATTCTGATAGTATTTGTCATATATCTGGCGTATGCGCAAGCAAATATCATAATCATGCA
TCAGCAGAAGTTGAAATTGAAGTAAAATCAAATGTTGGAGTACTTAAGAATAAAGAGCTC
AAAGATGATATTCCTTGTGAATTATGTGAACAGTTGGTCAAACATTTAAGTGATATTCTT
GTTGCAAATACAACTGAAACTGAATTTAAAAGCGTCCTTCAAGGTCTTTGTTCACAAACA
AAAGGATTCAAGAGCGAATGTTTAGAACTGGTAAATCAATATTATGCAATTATTTACGAG
TCTCTCGTTAATAATCTCGACGCAAATGGAGCTTGCTTTTTAATTGGAGTATGTCGCAAG
GGAGATAATAATCATCAAGTCACTCCACACATGCCA

>g602.t8 Gene=g602 Length=352
MKILFSIISSIVSSSVILGREKCTYGPSYWCNNLVNAKNCGAVKHCIKTVWEKQHVPEDT
DSICKICLDMVTQARDQLESNETQEELKEVFDGSCDLIPIKVVKTECKRLADDFIPELVE
ALASQMNPQVVCSTAGLCNNAKIDALLEEYEMQKKNNLLSCNQCNNIGELITQKFHTSSR
DQVLDGFLSACGRLSSFSDACSSIILTYFNEIYEELSRNLNSDSICHISGVCASKYHNHA
SAEVEIEVKSNVGVLKNKELKDDIPCELCEQLVKHLSDILVANTTETEFKSVLQGLCSQT
KGFKSECLELVNQYYAIIYESLVNNLDANGACFLIGVCRKGDNNHQVTPHMP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g602.t8 Gene3D G3DSA:1.10.225.10 Saposin 58 141 9.1E-20
18 g602.t8 Gene3D G3DSA:1.10.225.10 Saposin 157 241 2.7E-11
17 g602.t8 Gene3D G3DSA:1.10.225.10 Saposin 260 340 1.3E-17
7 g602.t8 PANTHER PTHR11480 SAPOSIN-RELATED 13 346 6.1E-69
8 g602.t8 PANTHER PTHR11480:SF84 BCDNA.GH08312 13 346 6.1E-69
10 g602.t8 PRINTS PR01797 Saposin signature 16 40 6.3E-10
11 g602.t8 PRINTS PR01797 Saposin signature 45 65 6.3E-10
9 g602.t8 PRINTS PR01797 Saposin signature 128 146 6.3E-10
6 g602.t8 Pfam PF02199 Saposin A-type domain 21 52 5.8E-16
1 g602.t8 Pfam PF05184 Saposin-like type B, region 1 63 99 2.3E-9
4 g602.t8 Pfam PF03489 Saposin-like type B, region 2 105 138 1.7E-9
3 g602.t8 Pfam PF03489 Saposin-like type B, region 2 200 232 1.4E-4
2 g602.t8 Pfam PF05184 Saposin-like type B, region 1 265 299 3.9E-7
5 g602.t8 Pfam PF03489 Saposin-like type B, region 2 306 338 8.1E-6
20 g602.t8 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
21 g602.t8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
22 g602.t8 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
23 g602.t8 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
19 g602.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 352 -
28 g602.t8 ProSiteProfiles PS51110 Saposin A-type domain profile. 16 56 14.931
31 g602.t8 ProSiteProfiles PS50015 Saposin B type domain profile. 60 142 20.297
29 g602.t8 ProSiteProfiles PS50015 Saposin B type domain profile. 157 236 11.733
30 g602.t8 ProSiteProfiles PS50015 Saposin B type domain profile. 262 342 15.929
24 g602.t8 SMART SM00162 sapA_2 19 52 1.6E-13
27 g602.t8 SMART SM00741 sapb_4 62 138 2.2E-22
26 g602.t8 SMART SM00741 sapb_4 159 232 1.2E-5
25 g602.t8 SMART SM00741 sapb_4 264 338 1.0E-15
14 g602.t8 SUPERFAMILY SSF47862 Saposin 61 140 5.61E-18
13 g602.t8 SUPERFAMILY SSF47862 Saposin 159 236 5.49E-10
12 g602.t8 SUPERFAMILY SSF47862 Saposin 262 339 2.47E-16
15 g602.t8 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -

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:0006665 sphingolipid metabolic process BP
GO:0005764 lysosome CC
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