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.t16 TSS g602.t16 4434335 4434335
chr_3 g602 g602.t16 isoform g602.t16 4434385 4437608
chr_3 g602 g602.t16 exon g602.t16.exon1 4434385 4434424
chr_3 g602 g602.t16 exon g602.t16.exon2 4434520 4434598
chr_3 g602 g602.t16 exon g602.t16.exon3 4434886 4435172
chr_3 g602 g602.t16 exon g602.t16.exon4 4435272 4437497
chr_3 g602 g602.t16 cds g602.t16.CDS1 4435338 4437497
chr_3 g602 g602.t16 exon g602.t16.exon5 4437561 4437608
chr_3 g602 g602.t16 cds g602.t16.CDS2 4437561 4437608
chr_3 g602 g602.t16 TTS g602.t16 4437776 4437776

Sequences

>g602.t16 Gene=g602 Length=2680
ATGAAGATTTTGTTCTCAATTATTTGTACTTTTTTGTTCGCGTCTATTGTATCTAGTTCC
GTTATATTGGGACGAGAAAAATGCACATACGGGCCCTCATATTGGTGTAATAACTTAGTA
AATGCAAAAAATTGCGGAGCAGTTAAACACTGTATTAAAACAGTTTGGGAAAAACAACAT
GTACCGGAAGACACTGATTCTATTTGCAAAATTTGTCTTGACATGGTAACCCAAGCCAGA
GATCAACTCGAAAGCAATGAAACTCAAGAAGAGTTGAAAGAAGTTTTCGATGGTTCTTGC
GATTTGATACCGATAAAAGTAGTAAAAACGGAATGCAAACGTTTGGCTGATGATTTCATA
CCAGAACTTGTTGAGGCACTTGCTTCTCAAATGAATCCACAGGCAAGTCGTTTGTTCTAC
AGCTGGACTTTGTAATAATGCAAAGATTGATGCATTATTGGAAGAATATGAAATGCAGAA
GAAAAATAATTTATTAAGTTGCAACCAATGTAACAACATTGGAGAATTGATCACTCAAAA
ATTCCATACATCATCTCGTGATCAAGTTCTAGATGGTTTCTTGAGTGCCTGCGGTCGTCT
TTCATCGTTTTCTGATGCATGTTCTAGTATCATTCTGACTTATTTCAACGAAATCTATGA
AGAACTTTCGAGAAATCTAAATTCTGATAGTATTTGTCATATATCTGGCGTATGCGCAAG
CAAATATCATAATCATGCATCAGCAGAAGTTGAAATTGAAGTAAAATCAAATGTTGGAGT
ACTTAAGAATAAAGAGCTCAAAGATGATATTCCTTGTGAATTATGTGAACAGTTGGTCAA
ACATTTAAGTGATATTCTTGTTGCAAATACAACTGAAACTGAATTTAAAAGCGTCCTTCA
AGGTCTTTGTTCACAAACAAAAGGATTCAAGAGCGAATGTTTAGAACTGGTAAATCAATA
TTATGCAATTATTTACGAGTCTCTCGTTAATAATCTCGACGCAAATGGAGCTTGCTTTTT
AATTGGAGTATGTCGCAAGGGAGATAATAATCATCAAGTCACTCCACACATGCCATTATT
GCCTACTAATCAAAAGAATATACCAAAGCGCAATCGATTAGGAGAGAATGAAAAATCCTA
TACAAATGAGCAAATCAAGAAAATGATTTTGCCTATTGATCAATTAATGGGAGCTAAATC
AAACCTTGATTTGGTTGATGGTGGTGAAAAGTGTACTCTTTGTCAATATTTTCTTCATTT
TGTTCAAGAAGAATTAAGTGATGCAAAAAATGAAGACGAAATTAAAGAGATAGTAGGAAA
AACTTGTGACAAATTCTCATCCGTAATTCGTTCAAATTGTCATCAATTTGTTAATTTATA
TGGAGATGCAATAATTGCTTTATTAGTTCAAAGCATTGATCCTCGCGATGTATGTCCCAA
TTTAAAATTATGTCCGAAATTCATGAATCAAGACGTTGATGTTTTTGCACCTTATCCGAT
CGTTGAAGTAAATGAATCCAGCAAAACGCAATGTCCATTGTGTGTTCTTGTTGTAAAAGA
GGCTCAAGATTATATAAAAAGTGAGAAAACTACTGAAACCGTAAAGAAAGCACTAGAAAG
AGCGTGTTCGAGACTCCCAGCAAAATTACAATTGCAATGTAAAGATTTTGTGGAAACTTA
TTACGATGAATTACTTCAAAAGTTGCTCTCTGATTTCACTCCAAAAGACATTTGCATTGA
TTTGCAATTGTGCACAAGAATTCAAGATGAAATAAAAGTTGGAATTGAAAAAGTCGAACA
TATTCCAAACATCAAGACAAATGAAATTCCTGATTATACTATCAACGGTCAATATTTTAC
AAGTTCTGATTCTGGAGAGTGCTTCTTGTGTACAACCGTTTTAAGTAACGCTGAGAGCAA
AATTACTCATGGAATGACTAAGAATCAAATTGAAGATATTTTATTACGCGAATGCTCAGT
TTATTATATTTATGAAGGCGTCTGCGATAATTTTGTTAAAACGAATATTGATCAAATATT
CTCTTTAGTAGAACAAAAACTTTCTCCTAAGCAAGTTTGTCAGAATTTATCTCTCTGTGC
ATCAACAGACGAGTTAAATATTGATGAAGCAGTTATTGTAAATGTTGTGGCATTACCTGC
ATTCCCAACTGAAAAGAAAAATGAATTTAATCGTGTTAAAATTATAAGAGGAGATGATGA
TGATGATGATGATGATGACGACGACGATGATGATGATGATGATGATGATGATGATGATCC
AAAGAAAAAACCTTCATTCAAAGATGATCCAATTTGTGTACTTTGCGAATTTGTAATGAC
AAAATTAGAATCTGAATTGAAAAATAAAAAAACACAGGAAGAAATCAAAGAGGCTGTTGA
GAATATTTGCTCAAAAATGCCGAAATCTGTTTCTAAGCAATGTACAAAATTCGTTGATCA
ATACAGTGAACTCATCATTGCATTGATTGATACTGTACCACCCAAAGAAATTTGTTCACA
AATGGGCTTATGTACAGCTGTAAAAAAACAAATGCACCTCGTGGGTGCAAATGAGTGCAC
TTATGGTCCAACTCACTTTTGTTCTGATATGAAAATTGCTGAAAAATGCAAGGCTACCAA
ATACTGTAAGGAAAAGAAGTTGGGAAAATTTTCAGTTTGA

>g602.t16 Gene=g602 Length=735
MQKKNNLLSCNQCNNIGELITQKFHTSSRDQVLDGFLSACGRLSSFSDACSSIILTYFNE
IYEELSRNLNSDSICHISGVCASKYHNHASAEVEIEVKSNVGVLKNKELKDDIPCELCEQ
LVKHLSDILVANTTETEFKSVLQGLCSQTKGFKSECLELVNQYYAIIYESLVNNLDANGA
CFLIGVCRKGDNNHQVTPHMPLLPTNQKNIPKRNRLGENEKSYTNEQIKKMILPIDQLMG
AKSNLDLVDGGEKCTLCQYFLHFVQEELSDAKNEDEIKEIVGKTCDKFSSVIRSNCHQFV
NLYGDAIIALLVQSIDPRDVCPNLKLCPKFMNQDVDVFAPYPIVEVNESSKTQCPLCVLV
VKEAQDYIKSEKTTETVKKALERACSRLPAKLQLQCKDFVETYYDELLQKLLSDFTPKDI
CIDLQLCTRIQDEIKVGIEKVEHIPNIKTNEIPDYTINGQYFTSSDSGECFLCTTVLSNA
ESKITHGMTKNQIEDILLRECSVYYIYEGVCDNFVKTNIDQIFSLVEQKLSPKQVCQNLS
LCASTDELNIDEAVIVNVVALPAFPTEKKNEFNRVKIIRGDDDDDDDDDDDDDDDDDDDD
DDPKKKPSFKDDPICVLCEFVMTKLESELKNKKTQEEIKEAVENICSKMPKSVSKQCTKF
VDQYSELIIALIDTVPPKEICSQMGLCTAVKKQMHLVGANECTYGPTHFCSDMKIAEKCK
ATKYCKEKKLGKFSV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
35 g602.t16 Coils Coil Coil 624 644 -
33 g602.t16 Gene3D G3DSA:1.10.225.10 Saposin 6 90 8.5E-11
31 g602.t16 Gene3D G3DSA:1.10.225.10 Saposin 109 189 4.0E-17
32 g602.t16 Gene3D G3DSA:1.10.225.10 Saposin 250 327 3.1E-21
30 g602.t16 Gene3D G3DSA:1.10.225.10 Saposin 349 429 1.1E-20
29 g602.t16 Gene3D G3DSA:1.10.225.10 Saposin 465 548 7.2E-16
34 g602.t16 Gene3D G3DSA:1.10.225.10 Saposin 609 689 2.9E-23
44 g602.t16 MobiDBLite mobidb-lite consensus disorder prediction 581 606 -
43 g602.t16 MobiDBLite mobidb-lite consensus disorder prediction 582 601 -
14 g602.t16 PANTHER PTHR11480 SAPOSIN-RELATED 2 197 1.1E-114
17 g602.t16 PANTHER PTHR11480:SF84 BCDNA.GH08312 2 197 1.1E-114
13 g602.t16 PANTHER PTHR11480 SAPOSIN-RELATED 230 433 1.1E-114
16 g602.t16 PANTHER PTHR11480:SF84 BCDNA.GH08312 230 433 1.1E-114
12 g602.t16 PANTHER PTHR11480 SAPOSIN-RELATED 465 690 1.1E-114
15 g602.t16 PANTHER PTHR11480:SF84 BCDNA.GH08312 465 690 1.1E-114
21 g602.t16 PRINTS PR01797 Saposin signature 99 119 8.5E-11
20 g602.t16 PRINTS PR01797 Saposin signature 129 146 8.5E-11
18 g602.t16 PRINTS PR01797 Saposin signature 354 374 8.5E-11
19 g602.t16 PRINTS PR01797 Saposin signature 403 421 8.5E-11
23 g602.t16 PRINTS PR01797 Saposin signature 467 489 8.5E-11
22 g602.t16 PRINTS PR01797 Saposin signature 520 543 8.5E-11
10 g602.t16 Pfam PF03489 Saposin-like type B, region 2 49 81 3.5E-4
2 g602.t16 Pfam PF05184 Saposin-like type B, region 1 114 148 9.9E-7
7 g602.t16 Pfam PF03489 Saposin-like type B, region 2 155 187 2.0E-5
4 g602.t16 Pfam PF05184 Saposin-like type B, region 1 253 288 2.4E-7
5 g602.t16 Pfam PF03489 Saposin-like type B, region 2 296 327 1.1E-7
3 g602.t16 Pfam PF05184 Saposin-like type B, region 1 353 389 1.0E-10
9 g602.t16 Pfam PF03489 Saposin-like type B, region 2 395 427 1.0E-9
8 g602.t16 Pfam PF03489 Saposin-like type B, region 2 510 542 2.7E-8
1 g602.t16 Pfam PF05184 Saposin-like type B, region 1 613 650 1.6E-13
6 g602.t16 Pfam PF03489 Saposin-like type B, region 2 655 687 1.2E-9
11 g602.t16 Pfam PF02199 Saposin A-type domain 700 728 9.1E-9
48 g602.t16 ProSiteProfiles PS50015 Saposin B type domain profile. 6 85 11.733
49 g602.t16 ProSiteProfiles PS50015 Saposin B type domain profile. 111 191 15.929
50 g602.t16 ProSiteProfiles PS50015 Saposin B type domain profile. 250 331 17.318
51 g602.t16 ProSiteProfiles PS50015 Saposin B type domain profile. 350 431 19.58
46 g602.t16 ProSiteProfiles PS50015 Saposin B type domain profile. 466 546 15.258
47 g602.t16 ProSiteProfiles PS50015 Saposin B type domain profile. 611 691 19.907
45 g602.t16 ProSiteProfiles PS51110 Saposin A-type domain profile. 695 735 10.22
41 g602.t16 SMART SM00741 sapb_4 8 81 1.2E-5
39 g602.t16 SMART SM00741 sapb_4 113 187 1.0E-15
42 g602.t16 SMART SM00741 sapb_4 252 327 4.0E-19
40 g602.t16 SMART SM00741 sapb_4 352 427 2.1E-22
37 g602.t16 SMART SM00741 sapb_4 468 542 1.2E-15
38 g602.t16 SMART SM00741 sapb_4 613 687 1.3E-25
36 g602.t16 SMART SM00162 sapA_2 698 731 0.0074
26 g602.t16 SUPERFAMILY SSF47862 Saposin 46 147 7.51E-15
28 g602.t16 SUPERFAMILY SSF47862 Saposin 152 288 1.18E-16
24 g602.t16 SUPERFAMILY SSF47862 Saposin 293 389 2.94E-19
25 g602.t16 SUPERFAMILY SSF47862 Saposin 467 544 3.27E-14
27 g602.t16 SUPERFAMILY SSF47862 Saposin 611 688 5.61E-20

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