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.t11 TSS g602.t11 4434335 4434335
chr_3 g602 g602.t11 isoform g602.t11 4434385 4435999
chr_3 g602 g602.t11 exon g602.t11.exon1 4434385 4434424
chr_3 g602 g602.t11 cds g602.t11.CDS1 4434385 4434424
chr_3 g602 g602.t11 exon g602.t11.exon2 4434520 4434598
chr_3 g602 g602.t11 cds g602.t11.CDS2 4434520 4434598
chr_3 g602 g602.t11 exon g602.t11.exon3 4434886 4435165
chr_3 g602 g602.t11 cds g602.t11.CDS3 4434886 4435165
chr_3 g602 g602.t11 exon g602.t11.exon4 4435272 4435999
chr_3 g602 g602.t11 cds g602.t11.CDS4 4435272 4435997
chr_3 g602 g602.t11 TTS g602.t11 NA NA

Sequences

>g602.t11 Gene=g602 Length=1127
ATGAAGATTTTGTTCTCAATTATTTGTACTTTTTTGTTCGCGTCTATTGTATCTAGTTCC
GTTATATTGGGACGAGAAAAATGCACATACGGGCCCTCATATTGGTGTAATAACTTAGTA
AATGCAAAAAATTGCGGAGCAGTTAAACACTGTATTAAAACAGTTTGGGAAAAACAACAT
GTACCGGAAGACACTGATTCTATTTGCAAAATTTGTCTTGACATGGTAACCCAAGCCAGA
GATCAACTCGAAAGCAATGAAACTCAAGAAGAGTTGAAAGAAGTTTTCGATGGTTCTTGC
GATTTGATACCGATAAAAGTAGTAAAAACGGAATGCAAACGTTTGGCTGATGATTTCATA
CCAGAACTTGTTGAGGCACTTGCTTCTCAAATGAATCCAGTCGTTTGTTCTACAGCTGGA
CTTTGTAATAATGCAAAGATTGATGCATTATTGGAAGAATATGAAATGCAGAAGAAAAAT
AATTTATTAAGTTGCAACCAATGTAACAACATTGGAGAATTGATCACTCAAAAATTCCAT
ACATCATCTCGTGATCAAGTTCTAGATGGTTTCTTGAGTGCCTGCGGTCGTCTTTCATCG
TTTTCTGATGCATGTTCTAGTATCATTCTGACTTATTTCAACGAAATCTATGAAGAACTT
TCGAGAAATCTAAATTCTGATAGTATTTGTCATATATCTGGCGTATGCGCAAGCAAATAT
CATAATCATGCATCAGCAGAAGTTGAAATTGAAGTAAAATCAAATGTTGGAGTACTTAAG
AATAAAGAGCTCAAAGATGATATTCCTTGTGAATTATGTGAACAGTTGGTCAAACATTTA
AGTGATATTCTTGTTGCAAATACAACTGAAACTGAATTTAAAAGCGTCCTTCAAGGTCTT
TGTTCACAAACAAAAGGATTCAAGAGCGAATGTTTAGAACTGGTAAATCAATATTATGCA
ATTATTTACGAGTCTCTCGTTAATAATCTCGACGCAAATGGAGCTTGCTTTTTAATTGGA
GTATGTCGCAAGGGAGATAATAATCATCAAGTCACTCCACACATGCCATTATTGCCTACT
AATCAAAAGAATATACCAAAGCGCAATCGATTAGGAGAGAATGAAAA

>g602.t11 Gene=g602 Length=375
MKILFSIICTFLFASIVSSSVILGREKCTYGPSYWCNNLVNAKNCGAVKHCIKTVWEKQH
VPEDTDSICKICLDMVTQARDQLESNETQEELKEVFDGSCDLIPIKVVKTECKRLADDFI
PELVEALASQMNPVVCSTAGLCNNAKIDALLEEYEMQKKNNLLSCNQCNNIGELITQKFH
TSSRDQVLDGFLSACGRLSSFSDACSSIILTYFNEIYEELSRNLNSDSICHISGVCASKY
HNHASAEVEIEVKSNVGVLKNKELKDDIPCELCEQLVKHLSDILVANTTETEFKSVLQGL
CSQTKGFKSECLELVNQYYAIIYESLVNNLDANGACFLIGVCRKGDNNHQVTPHMPLLPT
NQKNIPKRNRLGENE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g602.t11 Gene3D G3DSA:1.10.225.10 Saposin 63 145 4.4E-17
17 g602.t11 Gene3D G3DSA:1.10.225.10 Saposin 161 245 3.0E-11
19 g602.t11 Gene3D G3DSA:1.10.225.10 Saposin 264 344 1.5E-17
29 g602.t11 MobiDBLite mobidb-lite consensus disorder prediction 353 375 -
30 g602.t11 MobiDBLite mobidb-lite consensus disorder prediction 353 367 -
7 g602.t11 PANTHER PTHR11480 SAPOSIN-RELATED 9 351 2.4E-66
8 g602.t11 PANTHER PTHR11480:SF84 BCDNA.GH08312 9 351 2.4E-66
11 g602.t11 PRINTS PR01797 Saposin signature 21 45 2.8E-8
9 g602.t11 PRINTS PR01797 Saposin signature 50 70 2.8E-8
10 g602.t11 PRINTS PR01797 Saposin signature 132 150 2.8E-8
6 g602.t11 Pfam PF02199 Saposin A-type domain 26 57 6.3E-16
1 g602.t11 Pfam PF05184 Saposin-like type B, region 1 68 104 2.5E-9
4 g602.t11 Pfam PF03489 Saposin-like type B, region 2 110 142 3.5E-4
3 g602.t11 Pfam PF03489 Saposin-like type B, region 2 204 236 1.5E-4
2 g602.t11 Pfam PF05184 Saposin-like type B, region 1 269 303 4.3E-7
5 g602.t11 Pfam PF03489 Saposin-like type B, region 2 310 342 8.8E-6
21 g602.t11 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
22 g602.t11 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
23 g602.t11 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
24 g602.t11 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
20 g602.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 375 -
31 g602.t11 ProSiteProfiles PS51110 Saposin A-type domain profile. 21 61 14.931
33 g602.t11 ProSiteProfiles PS50015 Saposin B type domain profile. 65 146 17.224
32 g602.t11 ProSiteProfiles PS50015 Saposin B type domain profile. 161 240 11.733
34 g602.t11 ProSiteProfiles PS50015 Saposin B type domain profile. 266 346 15.929
25 g602.t11 SMART SM00162 sapA_2 24 57 1.6E-13
28 g602.t11 SMART SM00741 sapb_4 67 142 5.4E-18
27 g602.t11 SMART SM00741 sapb_4 163 236 1.2E-5
26 g602.t11 SMART SM00741 sapb_4 268 342 1.0E-15
13 g602.t11 SUPERFAMILY SSF47862 Saposin 66 144 8.3E-15
14 g602.t11 SUPERFAMILY SSF47862 Saposin 163 240 6.12E-10
12 g602.t11 SUPERFAMILY SSF47862 Saposin 266 343 2.69E-16
16 g602.t11 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
15 g602.t11 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