Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein lap4.

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_1 g11970 g11970.t7 isoform g11970.t7 19963298 19975393
chr_1 g11970 g11970.t7 exon g11970.t7.exon1 19963298 19963512
chr_1 g11970 g11970.t7 exon g11970.t7.exon2 19964002 19964493
chr_1 g11970 g11970.t7 cds g11970.t7.CDS1 19964332 19964493
chr_1 g11970 g11970.t7 exon g11970.t7.exon3 19969370 19969487
chr_1 g11970 g11970.t7 cds g11970.t7.CDS2 19969370 19969487
chr_1 g11970 g11970.t7 exon g11970.t7.exon4 19973977 19974145
chr_1 g11970 g11970.t7 cds g11970.t7.CDS3 19973977 19974145
chr_1 g11970 g11970.t7 exon g11970.t7.exon5 19974980 19975393
chr_1 g11970 g11970.t7 cds g11970.t7.CDS4 19974980 19975391
chr_1 g11970 g11970.t7 TSS g11970.t7 NA NA
chr_1 g11970 g11970.t7 TTS g11970.t7 NA NA

Sequences

>g11970.t7 Gene=g11970 Length=1408
TGTTTATTTTTTCACGATTTAAACATTTATTTTATTTGATTATGTTGGCAGAGAGACAGA
CACGAAAAGTGTGTAAAAAATTTCACTCTAACGTTCAGCTTTAAATGAGTGTGTTTAGTT
CTTGTGGCTGAACGATAGAAAAGAATTTCGCAGAAAATTTTAATATTAGTTTTTATAATA
AAATTAGCGGTGTAAATTGTAAATTTTATGATAAATTAAGAATACGCGAGCGGAGAGGAG
AAAAAATCGGGGTGTTGTCCATTATAAAATCAAAATATCAGAAAAAGTGAAAAATTAAGA
AAGACAAAAAATTAATGAGTTAATCGTTGCTGATAGTGAGGGGAGTTTTTTGTTCTTCAA
AAAGTTTCGAGCGACGGGAACCAAGTGTGAAAAAATGTAGATCAAAAGTGCCAAAAAAGC
AAATAAATTGAAATAAAAAATATAAAAGATATTTTTTTAAAAGAAAGCAAAATTGAGTGA
AAAAAGGCAAAAAAAAATCAGAGTTTGTAGTTTAGTGAAAAGTGCAAGAAAAAAAAAATT
CAACAATGTTTAAGTGCATTCCCATATTCAAAGGATGTAATCGACAAGTGGAGTTTGTGG
ATAAAAGACACTGCTCCTTACCAAATGTTCCCGAGGAAATTTTACGCTATTCAAGGAGTC
TCGAGGAATTGCTACTTGATGCAAATCATATTCGAGATTTGCCCAAGAATTTTTTCCGAT
TACATCGATTACGAAAGCTCGGCCTGAGTGACAATGAAATTCATAAACTTCCACCTGATA
TACAAAATTTTGAAAATCTTGTAGAATTAGACGTATCAAGAAATGATATTCCTGACATTC
CAGATGACATTCGCCATTTACGGCTTTTACAGATTGCTGATTTCAGCTCAAATCCTATTC
CAAAATTACCAGCTGGTTTCTCACAGCTTAAAAGTTTGACAATATTAGGATTAAATGACA
TGTCCTTGACCTCATTGCCAGCTGATTTTGGATGCTTAACACAATTGGAGTCACTAGAAT
TGCGCGAAAATCTTCTTAAAAATCTTCCCGAGTCAATAAGTCAGTTAACAAAACTCGAGC
GTTTAGATTTGGGCGATAATGAAATAGAAGAATTGCCGCCACATTTGGGTGATTTACCAT
CACTGCAAGAACTATGGCTCGATCATAATCAATTGCAGCGACTGCCGCCCGAAATTGGTA
AACTAAAGAATCTTATGTGTTTGGATGTGTCAGAAAATCGTCTTGAAGATTTACCTGAAG
AAATTGGAGGCTTAGAAAATCTTACTGATTTGCACTTGTCACAAAATCTTCTTGAATTTA
TACCAAATGGTATTGAGAAGTTGACTAAATTGACAATATTAAAGTTGGACCAAAATCGCT
TGCATGTTCTTAATGAAAGCATTGGAAT

>g11970.t7 Gene=g11970 Length=287
MFKCIPIFKGCNRQVEFVDKRHCSLPNVPEEILRYSRSLEELLLDANHIRDLPKNFFRLH
RLRKLGLSDNEIHKLPPDIQNFENLVELDVSRNDIPDIPDDIRHLRLLQIADFSSNPIPK
LPAGFSQLKSLTILGLNDMSLTSLPADFGCLTQLESLELRENLLKNLPESISQLTKLERL
DLGDNEIEELPPHLGDLPSLQELWLDHNQLQRLPPEIGKLKNLMCLDVSENRLEDLPEEI
GGLENLTDLHLSQNLLEFIPNGIEKLTKLTILKLDQNRLHVLNESIG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
27 g11970.t7 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 2 120 0.000
29 g11970.t7 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 121 184 0.000
28 g11970.t7 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 185 285 0.000
3 g11970.t7 PANTHER PTHR23119:SF44 PROTEIN SCRIBBLE HOMOLOG 1 287 0.000
4 g11970.t7 PANTHER PTHR23119 DISCS LARGE 1 287 0.000
1 g11970.t7 Pfam PF13855 Leucine rich repeat 37 95 0.000
2 g11970.t7 Pfam PF13855 Leucine rich repeat 198 256 0.000
30 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 38 59 6.942
31 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 61 82 6.888
37 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 84 105 7.596
34 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 107 129 4.932
35 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 130 151 4.932
38 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 153 174 6.957
39 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 176 198 7.712
40 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 199 220 7.812
36 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 222 243 6.888
32 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 245 267 7.150
33 g11970.t7 ProSiteProfiles PS51450 Leucine-rich repeat profile. 268 287 5.317
10 g11970.t7 SMART SM00364 LRR_bac_2 36 55 85.000
11 g11970.t7 SMART SM00369 LRR_typ_2 37 58 92.000
17 g11970.t7 SMART SM00369 LRR_typ_2 59 81 2.200
26 g11970.t7 SMART SM00365 LRR_sd22_2 59 84 130.000
18 g11970.t7 SMART SM00369 LRR_typ_2 82 104 17.000
19 g11970.t7 SMART SM00369 LRR_typ_2 105 127 250.000
21 g11970.t7 SMART SM00369 LRR_typ_2 128 150 41.000
8 g11970.t7 SMART SM00364 LRR_bac_2 151 170 48.000
14 g11970.t7 SMART SM00369 LRR_typ_2 151 173 14.000
23 g11970.t7 SMART SM00365 LRR_sd22_2 151 173 94.000
7 g11970.t7 SMART SM00364 LRR_bac_2 174 193 230.000
13 g11970.t7 SMART SM00369 LRR_typ_2 174 196 0.260
22 g11970.t7 SMART SM00365 LRR_sd22_2 174 192 14.000
9 g11970.t7 SMART SM00364 LRR_bac_2 197 216 120.000
12 g11970.t7 SMART SM00369 LRR_typ_2 197 219 0.007
24 g11970.t7 SMART SM00365 LRR_sd22_2 197 225 300.000
6 g11970.t7 SMART SM00364 LRR_bac_2 220 239 25.000
16 g11970.t7 SMART SM00369 LRR_typ_2 220 242 6.700
15 g11970.t7 SMART SM00369 LRR_typ_2 243 265 1.700
25 g11970.t7 SMART SM00365 LRR_sd22_2 243 265 320.000
20 g11970.t7 SMART SM00369 LRR_typ_2 266 287 71.000
5 g11970.t7 SUPERFAMILY SSF52058 L domain-like 9 283 0.000

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

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.

Raw TPM values