Gene loci information

Transcript annotation

  • This transcript has been annotated as Phospholipase A-2-activating protein.

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 g2354 g2354.t1 TTS g2354.t1 17112451 17112451
chr_3 g2354 g2354.t1 isoform g2354.t1 17112508 17114952
chr_3 g2354 g2354.t1 exon g2354.t1.exon1 17112508 17114005
chr_3 g2354 g2354.t1 cds g2354.t1.CDS1 17112508 17114005
chr_3 g2354 g2354.t1 exon g2354.t1.exon2 17114069 17114752
chr_3 g2354 g2354.t1 cds g2354.t1.CDS2 17114069 17114752
chr_3 g2354 g2354.t1 exon g2354.t1.exon3 17114819 17114952
chr_3 g2354 g2354.t1 cds g2354.t1.CDS3 17114819 17114952
chr_3 g2354 g2354.t1 TSS g2354.t1 17115008 17115008

Sequences

>g2354.t1 Gene=g2354 Length=2316
ATGGAAGAATTTAAGCTATCTGCTGAGTTATCTGGACATTCATTAGATGTAAGAGCAGTA
ACTTATGCGAATAATTGTATTATATCAGGTTCACGTGATAAAACAGCAAGAATTTTCGAA
AGAACTGATGATGGGAAAAACTTCAAGCAAACCGAAGTATTAACAAATCACTCTAATTTT
GTATCATCAGTGTGTGTTTTAAACGATGGAAACTGGCTTGCAACAGCCTCAAATGATAAA
ACTATTTGTTTGTATAATTTTGGTATTGTGCAACCTTTTGCTACTTTGAAAGAGCATACA
AGTACTGTTTGTTCATTAGCTCAAGGATTAGAATCGAAAATTCTTATAAGCGGAAGTTGG
GATCAAACAGCTAGAATTTGGAATAATTTAGATATTGATAGTTCATCGATTGAATTAAAT
GGGCATGAAGCTGCAGTTTGGGCAGTTTGTACTTTAAAAAATGGCAAATATGCTACTGGA
AGTGCTGATAAAAATATCTTTGTTTGGAATACAAGAGGTGAGAAATTAGTAGTCTTAAAA
GGACATACAGATTGCGTTAGAGCACTTGCTGCTTTGGATGATGGATCTCTTTTAAGTGCT
TCGAATGATGCAACAATTCGTCATTGGAGTGATACATATGATTGCATTAAAGAGTTTCAT
GGACACGCTAATTATATTTACTCAATTGCACTTAATCCTGCTCTTGGTGATCTCTTTGTA
ACTGGAAGTGAAGACAATACAATAAGATTGTGGTCAGTCAGTAAAGGTGCTCTTGGTGAT
GCCATTTATTTGCCAGCTCAATCCGTTTGGGCTGTCGCATGCGCTGATAATGGAGACATT
ATTACTGGCTCAAGTGATGCACTTGTACGTGTATTTACAAAAGATCCTTCGAGAATGGCT
TCAGAAGAAACTATTTCTGCATTTGAAACTGCAGTTGCTACAAGAAAACTTGAACAAAGC
AAAGAATTAGGTGGTATAAAAGTCAATGATTTACCAGGACCTGAATCGTTATTGCAAGTA
GGTTCTGAAGGTCAAACTCGTTTAGTACGTCAACCTGATGGAAAAATACTCTGTTATCAA
TGGACAAAGGGAAAGTGGGAATGTGTTGGTGACGTAATGGGAGCAGCAGGAGGAACACAA
CAAACATCAGGAAAAAGTTTGCATGAAGGAAAAGAATATGATTATGTGTTTAATGTGGAT
ATAGAAGATGGTAAACCACCAATTAAACTTCCATTTAATGTAACTGAAGATCCGTGGATG
GCAGCTCAAAAATTTATTCATAAAAATGATTTACCCCAAGTTTATCTTGAACAAGTAGCA
AATTTCATAATAAAAAATGCTAGCTTAACAACAATGCCAGTTGCAAACGAATCTTTTGCT
GATCCTTTTACCGGTGGTGGACGTTATGTTCCTTCATCAAATGGTAATAATGTTCAAAGT
TCATCAAACAATGTCAATGTCAACTTTCGAGAAAGAACTGGTGGCAATTCTGGAGCAATT
AATCTCGATCCATTTACCGGTGGTTCAAGTTATTCATCAGGAAAGCGCGATTTAATAGTT
CAGAAACATATTCCATGTCTTAATTTATCCACATTTGATGCCTTTGATGGTTCAAAAATT
CTCGCAAAACTCAAAGAATTTAACAATCAGTTAGAAGATGAAAATCTGAAAGTAACAGAT
ACACAAATTGATAGCATCAATCAGCTATTTTCAAACAATGTCCCAGATGATGAAACTATT
AAAATTTTCAAAAAATTGTTGCAATGGCCAAATGATAAACTTTTTCCACTTCTTGACATT
CTTCGTTTAGGCGTTCGCAACAAAATAATTTGTGAGAAACTTGCATCAATTGATTATGTT
ATAGATAAAATCAGCACAACAGCAGCAAATCAATTAATGTCAATTAGAGCACTCAGTAAT
ATGTTAATTCATGAATATGGAAAAAATAGCGTTGAAGTTAAAATTATTAACATTTGCGAA
TCGATCTCAAAAATTTCACAAGGAAGTAGCAATCTTCAAAATGCAATAGCTACTTTCTTC
CTCAATCAATCTATATTGCAAAAGGATGTGAAATCAGAAGAAGTTTGTACAATTTTATTA
CTTGAATTATTGAGAGCTCTCGATTGGATTAGTGACCCAGAAGCAACATTCAAATCATAT
GCTGCAATTGGTAATTTAATTACATTCAACTCATCTGCTACTGTATCCATTATAAAATCT
ACAGAAAATTTTAAAAATTCTCTAGAACGAAATCGAAGTGCTCAATATGAAAAGTTGGCT
GAAATATCTAATGAATTGACTGAAAAACTTCTTTGA

>g2354.t1 Gene=g2354 Length=771
MEEFKLSAELSGHSLDVRAVTYANNCIISGSRDKTARIFERTDDGKNFKQTEVLTNHSNF
VSSVCVLNDGNWLATASNDKTICLYNFGIVQPFATLKEHTSTVCSLAQGLESKILISGSW
DQTARIWNNLDIDSSSIELNGHEAAVWAVCTLKNGKYATGSADKNIFVWNTRGEKLVVLK
GHTDCVRALAALDDGSLLSASNDATIRHWSDTYDCIKEFHGHANYIYSIALNPALGDLFV
TGSEDNTIRLWSVSKGALGDAIYLPAQSVWAVACADNGDIITGSSDALVRVFTKDPSRMA
SEETISAFETAVATRKLEQSKELGGIKVNDLPGPESLLQVGSEGQTRLVRQPDGKILCYQ
WTKGKWECVGDVMGAAGGTQQTSGKSLHEGKEYDYVFNVDIEDGKPPIKLPFNVTEDPWM
AAQKFIHKNDLPQVYLEQVANFIIKNASLTTMPVANESFADPFTGGGRYVPSSNGNNVQS
SSNNVNVNFRERTGGNSGAINLDPFTGGSSYSSGKRDLIVQKHIPCLNLSTFDAFDGSKI
LAKLKEFNNQLEDENLKVTDTQIDSINQLFSNNVPDDETIKIFKKLLQWPNDKLFPLLDI
LRLGVRNKIICEKLASIDYVIDKISTTAANQLMSIRALSNMLIHEYGKNSVEVKIINICE
SISKISQGSSNLQNAIATFFLNQSILQKDVKSEEVCTILLLELLRALDWISDPEATFKSY
AAIGNLITFNSSATVSIIKSTENFKNSLERNRSAQYEKLAEISNELTEKLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g2354.t1 CDD cd00200 WD40 6 292 1.28095E-64
18 g2354.t1 Coils Coil Coil 544 564 -
19 g2354.t1 Coils Coil Coil 745 765 -
15 g2354.t1 Gene3D G3DSA:2.130.10.10 - 1 312 1.9E-84
17 g2354.t1 Gene3D G3DSA:1.10.150.410 - 378 456 7.8E-35
16 g2354.t1 Gene3D G3DSA:1.25.10.10 - 521 770 3.7E-42
9 g2354.t1 PANTHER PTHR19849:SF0 PHOSPHOLIPASE A2-ACTIVATING PROTEIN 1 755 4.7E-198
10 g2354.t1 PANTHER PTHR19849 PHOSPHOLIPASE A-2-ACTIVATING PROTEIN 1 755 4.7E-198
11 g2354.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 115 129 1.7E-5
13 g2354.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 157 171 1.7E-5
12 g2354.t1 PRINTS PR00320 G protein beta WD-40 repeat signature 239 253 1.7E-5
3 g2354.t1 Pfam PF00400 WD domain, G-beta repeat 6 39 0.2
2 g2354.t1 Pfam PF00400 WD domain, G-beta repeat 51 86 1.9E-5
6 g2354.t1 Pfam PF00400 WD domain, G-beta repeat 91 128 3.5E-4
5 g2354.t1 Pfam PF00400 WD domain, G-beta repeat 138 170 4.7E-4
4 g2354.t1 Pfam PF00400 WD domain, G-beta repeat 174 210 0.0042
7 g2354.t1 Pfam PF00400 WD domain, G-beta repeat 214 252 1.1E-5
8 g2354.t1 Pfam PF09070 PFU (PLAA family ubiquitin binding) 342 448 4.1E-39
1 g2354.t1 Pfam PF08324 PUL domain 525 753 2.0E-36
28 g2354.t1 ProSitePatterns PS00678 Trp-Asp (WD) repeats signature. 115 129 -
30 g2354.t1 ProSiteProfiles PS50294 Trp-Asp (WD) repeats circular profile. 10 302 33.326
32 g2354.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 54 86 9.539
35 g2354.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 96 128 11.177
34 g2354.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 139 179 9.339
33 g2354.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 179 210 9.205
31 g2354.t1 ProSiteProfiles PS50082 Trp-Asp (WD) repeats profile. 219 261 14.686
29 g2354.t1 ProSiteProfiles PS51394 PFU domain profile. 358 457 42.044
36 g2354.t1 ProSiteProfiles PS51396 PUL domain profile. 522 769 19.845
24 g2354.t1 SMART SM00320 WD40_4 3 40 0.0023
27 g2354.t1 SMART SM00320 WD40_4 47 86 9.6E-8
26 g2354.t1 SMART SM00320 WD40_4 89 128 1.0E-4
25 g2354.t1 SMART SM00320 WD40_4 132 170 5.3E-4
21 g2354.t1 SMART SM00320 WD40_4 172 210 2.3E-5
22 g2354.t1 SMART SM00320 WD40_4 212 252 7.4E-9
23 g2354.t1 SMART SM00320 WD40_4 255 293 17.0
14 g2354.t1 SUPERFAMILY SSF50978 WD40 repeat-like 4 308 4.48E-60

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:0005515 protein binding MF

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