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.t5 TSS g602.t5 4434335 4434335
chr_3 g602 g602.t5 isoform g602.t5 4434385 4435576
chr_3 g602 g602.t5 exon g602.t5.exon1 4434385 4434424
chr_3 g602 g602.t5 cds g602.t5.CDS1 4434385 4434424
chr_3 g602 g602.t5 exon g602.t5.exon2 4434520 4434598
chr_3 g602 g602.t5 cds g602.t5.CDS2 4434520 4434598
chr_3 g602 g602.t5 exon g602.t5.exon3 4434886 4435168
chr_3 g602 g602.t5 cds g602.t5.CDS3 4434886 4435168
chr_3 g602 g602.t5 exon g602.t5.exon4 4435272 4435576
chr_3 g602 g602.t5 cds g602.t5.CDS4 4435272 4435574
chr_3 g602 g602.t5 TTS g602.t5 NA NA

Sequences

>g602.t5 Gene=g602 Length=707
ATGAAGATTTTGTTCTCAATTATTTGTACTTTTTTGTTCGCGTCTATTGTATCTAGTTCC
GTTATATTGGGACGAGAAAAATGCACATACGGGCCCTCATATTGGTGTAATAACTTAGTA
AATGCAAAAAATTGCGGAGCAGTTAAACACTGTATTAAAACAGTTTGGGAAAAACAACAT
GTACCGGAAGACACTGATTCTATTTGCAAAATTTGTCTTGACATGGTAACCCAAGCCAGA
GATCAACTCGAAAGCAATGAAACTCAAGAAGAGTTGAAAGAAGTTTTCGATGGTTCTTGC
GATTTGATACCGATAAAAGTAGTAAAAACGGAATGCAAACGTTTGGCTGATGATTTCATA
CCAGAACTTGTTGAGGCACTTGCTTCTCAAATGAATCCACAGGTCGTTTGTTCTACAGCT
GGACTTTGTAATAATGCAAAGATTGATGCATTATTGGAAGAATATGAAATGCAGAAGAAA
AATAATTTATTAAGTTGCAACCAATGTAACAACATTGGAGAATTGATCACTCAAAAATTC
CATACATCATCTCGTGATCAAGTTCTAGATGGTTTCTTGAGTGCCTGCGGTCGTCTTTCA
TCGTTTTCTGATGCATGTTCTAGTATCATTCTGACTTATTTCAACGAAATCTATGAAGAA
CTTTCGAGAAATCTAAATTCTGATAGTATTTGTCATATATCTGGCGT

>g602.t5 Gene=g602 Length=235
MKILFSIICTFLFASIVSSSVILGREKCTYGPSYWCNNLVNAKNCGAVKHCIKTVWEKQH
VPEDTDSICKICLDMVTQARDQLESNETQEELKEVFDGSCDLIPIKVVKTECKRLADDFI
PELVEALASQMNPQVVCSTAGLCNNAKIDALLEEYEMQKKNNLLSCNQCNNIGELITQKF
HTSSRDQVLDGFLSACGRLSSFSDACSSIILTYFNEIYEELSRNLNSDSICHISG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g602.t5 Gene3D G3DSA:1.10.225.10 Saposin 63 146 4.2E-20
14 g602.t5 Gene3D G3DSA:1.10.225.10 Saposin 162 235 3.8E-9
4 g602.t5 PANTHER PTHR11480 SAPOSIN-RELATED 9 231 4.5E-50
5 g602.t5 PANTHER PTHR11480:SF84 BCDNA.GH08312 9 231 4.5E-50
8 g602.t5 PRINTS PR01797 Saposin signature 21 45 2.4E-10
6 g602.t5 PRINTS PR01797 Saposin signature 50 70 2.4E-10
7 g602.t5 PRINTS PR01797 Saposin signature 133 151 2.4E-10
3 g602.t5 Pfam PF02199 Saposin A-type domain 26 57 3.3E-16
1 g602.t5 Pfam PF05184 Saposin-like type B, region 1 68 104 1.3E-9
2 g602.t5 Pfam PF03489 Saposin-like type B, region 2 110 143 9.5E-10
16 g602.t5 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
17 g602.t5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
18 g602.t5 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
19 g602.t5 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
15 g602.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 235 -
23 g602.t5 ProSiteProfiles PS51110 Saposin A-type domain profile. 21 61 14.931
25 g602.t5 ProSiteProfiles PS50015 Saposin B type domain profile. 65 147 20.297
24 g602.t5 ProSiteProfiles PS50015 Saposin B type domain profile. 162 235 10.017
20 g602.t5 SMART SM00162 sapA_2 24 57 1.6E-13
21 g602.t5 SMART SM00741 sapb_4 67 143 2.2E-22
22 g602.t5 SMART SM00741 sapb_4 164 233 0.2
10 g602.t5 SUPERFAMILY SSF47862 Saposin 66 145 2.58E-18
9 g602.t5 SUPERFAMILY SSF47862 Saposin 165 234 1.15E-9
12 g602.t5 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
11 g602.t5 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 24 -

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. There were no conditions that were differentially expressed