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.t15 TSS g602.t15 4434335 4434335
chr_3 g602 g602.t15 isoform g602.t15 4434385 4437148
chr_3 g602 g602.t15 exon g602.t15.exon1 4434385 4434424
chr_3 g602 g602.t15 exon g602.t15.exon2 4434520 4434598
chr_3 g602 g602.t15 exon g602.t15.exon3 4434886 4435163
chr_3 g602 g602.t15 exon g602.t15.exon4 4435272 4437148
chr_3 g602 g602.t15 cds g602.t15.CDS1 4435338 4437146
chr_3 g602 g602.t15 TTS g602.t15 4437776 4437776

Sequences

>g602.t15 Gene=g602 Length=2274
ATGAAGATTTTGTTCTCAATTATTTGTACTTTTTTGTTCGCGTCTATTGTATCTAGTTCC
GTTATATTGGGACGAGAAAAATGCACATACGGGCCCTCATATTGGTGTAATAACTTAGTA
AATGCAAAAAATTGCGGAGCAGTTAAACACTGTATTAAAACAGTTTGGGAAAAACAACAT
GTACCGGAAGACACTGATTCTATTTGCAAAATTTGTCTTGACATGGTAACCCAAGCCAGA
GATCAACTCGAAAGCAATGAAACTCAAGAAGAGTTGAAAGAAGTTTTCGATGGTTCTTGC
GATTTGATACCGATAAAAGTAGTAAAAACGGAATGCAAACGTTTGGCTGATGATTTCATA
CCAGAACTTGTTGAGGCACTTGCTTCTCAAATGAATCGTCGTTTGTTCTACAGCTGGACT
TTGTAATAATGCAAAGATTGATGCATTATTGGAAGAATATGAAATGCAGAAGAAAAATAA
TTTATTAAGTTGCAACCAATGTAACAACATTGGAGAATTGATCACTCAAAAATTCCATAC
ATCATCTCGTGATCAAGTTCTAGATGGTTTCTTGAGTGCCTGCGGTCGTCTTTCATCGTT
TTCTGATGCATGTTCTAGTATCATTCTGACTTATTTCAACGAAATCTATGAAGAACTTTC
GAGAAATCTAAATTCTGATAGTATTTGTCATATATCTGGCGTATGCGCAAGCAAATATCA
TAATCATGCATCAGCAGAAGTTGAAATTGAAGTAAAATCAAATGTTGGAGTACTTAAGAA
TAAAGAGCTCAAAGATGATATTCCTTGTGAATTATGTGAACAGTTGGTCAAACATTTAAG
TGATATTCTTGTTGCAAATACAACTGAAACTGAATTTAAAAGCGTCCTTCAAGGTCTTTG
TTCACAAACAAAAGGATTCAAGAGCGAATGTTTAGAACTGGTAAATCAATATTATGCAAT
TATTTACGAGTCTCTCGTTAATAATCTCGACGCAAATGGAGCTTGCTTTTTAATTGGAGT
ATGTCGCAAGGGAGATAATAATCATCAAGTCACTCCACACATGCCATTATTGCCTACTAA
TCAAAAGAATATACCAAAGCGCAATCGATTAGGAGAGAATGAAAAATCCTATACAAATGA
GCAAATCAAGAAAATGATTTTGCCTATTGATCAATTAATGGGAGCTAAATCAAACCTTGA
TTTGGTTGATGGTGGTGAAAAGTGTACTCTTTGTCAATATTTTCTTCATTTTGTTCAAGA
AGAATTAAGTGATGCAAAAAATGAAGACGAAATTAAAGAGATAGTAGGAAAAACTTGTGA
CAAATTCTCATCCGTAATTCGTTCAAATTGTCATCAATTTGTTAATTTATATGGAGATGC
AATAATTGCTTTATTAGTTCAAAGCATTGATCCTCGCGATGTATGTCCCAATTTAAAATT
ATGTCCGAAATTCATGAATCAAGACGTTGATGTTTTTGCACCTTATCCGATCGTTGAAGT
AAATGAATCCAGCAAAACGCAATGTCCATTGTGTGTTCTTGTTGTAAAAGAGGCTCAAGA
TTATATAAAAAGTGAGAAAACTACTGAAACCGTAAAGAAAGCACTAGAAAGAGCGTGTTC
GAGACTCCCAGCAAAATTACAATTGCAATGTAAAGATTTTGTGGAAACTTATTACGATGA
ATTACTTCAAAAGTTGCTCTCTGATTTCACTCCAAAAGACATTTGCATTGATTTGCAATT
GTGCACAAGAATTCAAGATGAAATAAAAGTTGGAATTGAAAAAGTCGAACATATTCCAAA
CATCAAGACAAATGAAATTCCTGATTATACTATCAACGGTCAATATTTTACAAGTTCTGA
TTCTGGAGAGTGCTTCTTGTGTACAACCGTTTTAAGTAACGCTGAGAGCAAAATTACTCA
TGGAATGACTAAGAATCAAATTGAAGATATTTTATTACGCGAATGCTCAGTTTATTATAT
TTATGAAGGCGTCTGCGATAATTTTGTTAAAACGAATATTGATCAAATATTCTCTTTAGT
AGAACAAAAACTTTCTCCTAAGCAAGTTTGTCAGAATTTATCTCTCTGTGCATCAACAGA
CGAGTTAAATATTGATGAAGCAGTTATTGTAAATGTTGTGGCATTACCTGCATTCCCAAC
TGAAAAGAAAAATGAATTTAATCGTGTTAAAATTATAAGAGGAGATGATGATGATGATGA
TGATGATGACGACGACGATGATGATGATGATGATGATGATGATGATGATCCAAA

>g602.t15 Gene=g602 Length=603
MQKKNNLLSCNQCNNIGELITQKFHTSSRDQVLDGFLSACGRLSSFSDACSSIILTYFNE
IYEELSRNLNSDSICHISGVCASKYHNHASAEVEIEVKSNVGVLKNKELKDDIPCELCEQ
LVKHLSDILVANTTETEFKSVLQGLCSQTKGFKSECLELVNQYYAIIYESLVNNLDANGA
CFLIGVCRKGDNNHQVTPHMPLLPTNQKNIPKRNRLGENEKSYTNEQIKKMILPIDQLMG
AKSNLDLVDGGEKCTLCQYFLHFVQEELSDAKNEDEIKEIVGKTCDKFSSVIRSNCHQFV
NLYGDAIIALLVQSIDPRDVCPNLKLCPKFMNQDVDVFAPYPIVEVNESSKTQCPLCVLV
VKEAQDYIKSEKTTETVKKALERACSRLPAKLQLQCKDFVETYYDELLQKLLSDFTPKDI
CIDLQLCTRIQDEIKVGIEKVEHIPNIKTNEIPDYTINGQYFTSSDSGECFLCTTVLSNA
ESKITHGMTKNQIEDILLRECSVYYIYEGVCDNFVKTNIDQIFSLVEQKLSPKQVCQNLS
LCASTDELNIDEAVIVNVVALPAFPTEKKNEFNRVKIIRGDDDDDDDDDDDDDDDDDDDD
DDP

Protein features from InterProScan

Transcript Database ID Name Start End E.value
29 g602.t15 Gene3D G3DSA:1.10.225.10 Saposin 6 90 6.4E-11
27 g602.t15 Gene3D G3DSA:1.10.225.10 Saposin 109 189 3.0E-17
28 g602.t15 Gene3D G3DSA:1.10.225.10 Saposin 250 327 2.4E-21
26 g602.t15 Gene3D G3DSA:1.10.225.10 Saposin 349 429 8.0E-21
25 g602.t15 Gene3D G3DSA:1.10.225.10 Saposin 465 548 5.4E-16
36 g602.t15 MobiDBLite mobidb-lite consensus disorder prediction 577 603 -
35 g602.t15 MobiDBLite mobidb-lite consensus disorder prediction 582 603 -
11 g602.t15 PANTHER PTHR11480 SAPOSIN-RELATED 2 197 2.4E-100
14 g602.t15 PANTHER PTHR11480:SF84 BCDNA.GH08312 2 197 2.4E-100
10 g602.t15 PANTHER PTHR11480 SAPOSIN-RELATED 230 445 2.4E-100
13 g602.t15 PANTHER PTHR11480:SF84 BCDNA.GH08312 230 445 2.4E-100
9 g602.t15 PANTHER PTHR11480 SAPOSIN-RELATED 348 548 2.4E-100
12 g602.t15 PANTHER PTHR11480:SF84 BCDNA.GH08312 348 548 2.4E-100
18 g602.t15 PRINTS PR01797 Saposin signature 99 119 2.9E-11
17 g602.t15 PRINTS PR01797 Saposin signature 129 146 2.9E-11
15 g602.t15 PRINTS PR01797 Saposin signature 354 374 2.9E-11
16 g602.t15 PRINTS PR01797 Saposin signature 403 421 2.9E-11
20 g602.t15 PRINTS PR01797 Saposin signature 467 489 2.9E-11
19 g602.t15 PRINTS PR01797 Saposin signature 520 543 2.9E-11
8 g602.t15 Pfam PF03489 Saposin-like type B, region 2 49 81 2.8E-4
1 g602.t15 Pfam PF05184 Saposin-like type B, region 1 114 148 7.8E-7
5 g602.t15 Pfam PF03489 Saposin-like type B, region 2 155 187 1.6E-5
3 g602.t15 Pfam PF05184 Saposin-like type B, region 1 253 288 1.9E-7
4 g602.t15 Pfam PF03489 Saposin-like type B, region 2 296 327 8.6E-8
2 g602.t15 Pfam PF05184 Saposin-like type B, region 1 353 389 8.2E-11
7 g602.t15 Pfam PF03489 Saposin-like type B, region 2 395 427 8.2E-10
6 g602.t15 Pfam PF03489 Saposin-like type B, region 2 510 542 2.1E-8
38 g602.t15 ProSiteProfiles PS50015 Saposin B type domain profile. 6 85 11.733
39 g602.t15 ProSiteProfiles PS50015 Saposin B type domain profile. 111 191 15.929
40 g602.t15 ProSiteProfiles PS50015 Saposin B type domain profile. 250 331 17.318
41 g602.t15 ProSiteProfiles PS50015 Saposin B type domain profile. 350 431 19.58
37 g602.t15 ProSiteProfiles PS50015 Saposin B type domain profile. 466 546 15.258
33 g602.t15 SMART SM00741 sapb_4 8 81 1.2E-5
31 g602.t15 SMART SM00741 sapb_4 113 187 1.0E-15
34 g602.t15 SMART SM00741 sapb_4 252 327 4.0E-19
32 g602.t15 SMART SM00741 sapb_4 352 427 2.1E-22
30 g602.t15 SMART SM00741 sapb_4 468 542 1.2E-15
23 g602.t15 SUPERFAMILY SSF47862 Saposin 46 147 5.61E-15
24 g602.t15 SUPERFAMILY SSF47862 Saposin 152 288 8.24E-17
21 g602.t15 SUPERFAMILY SSF47862 Saposin 293 389 2.26E-19
22 g602.t15 SUPERFAMILY SSF47862 Saposin 467 544 2.13E-14

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

Pathway

  • This transcript belongs to the following pathways

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