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.t9 TSS g11970.t9 19963419 19963419
chr_1 g11970 g11970.t9 isoform g11970.t9 19964332 19975830
chr_1 g11970 g11970.t9 exon g11970.t9.exon1 19964332 19964493
chr_1 g11970 g11970.t9 cds g11970.t9.CDS1 19964332 19964493
chr_1 g11970 g11970.t9 exon g11970.t9.exon2 19969370 19969487
chr_1 g11970 g11970.t9 cds g11970.t9.CDS2 19969370 19969487
chr_1 g11970 g11970.t9 exon g11970.t9.exon3 19973977 19974145
chr_1 g11970 g11970.t9 cds g11970.t9.CDS3 19973977 19974145
chr_1 g11970 g11970.t9 exon g11970.t9.exon4 19974980 19975393
chr_1 g11970 g11970.t9 cds g11970.t9.CDS4 19974980 19975393
chr_1 g11970 g11970.t9 exon g11970.t9.exon5 19975464 19975830
chr_1 g11970 g11970.t9 cds g11970.t9.CDS5 19975464 19975830
chr_1 g11970 g11970.t9 TTS g11970.t9 NA NA

Sequences

>g11970.t9 Gene=g11970 Length=1230
ATGTTTAAGTGCATTCCCATATTCAAAGGATGTAATCGACAAGTGGAGTTTGTGGATAAA
AGACACTGCTCCTTACCAAATGTTCCCGAGGAAATTTTACGCTATTCAAGGAGTCTCGAG
GAATTGCTACTTGATGCAAATCATATTCGAGATTTGCCCAAGAATTTTTTCCGATTACAT
CGATTACGAAAGCTCGGCCTGAGTGACAATGAAATTCATAAACTTCCACCTGATATACAA
AATTTTGAAAATCTTGTAGAATTAGACGTATCAAGAAATGATATTCCTGACATTCCAGAT
GACATTCGCCATTTACGGCTTTTACAGATTGCTGATTTCAGCTCAAATCCTATTCCAAAA
TTACCAGCTGGTTTCTCACAGCTTAAAAGTTTGACAATATTAGGATTAAATGACATGTCC
TTGACCTCATTGCCAGCTGATTTTGGATGCTTAACACAATTGGAGTCACTAGAATTGCGC
GAAAATCTTCTTAAAAATCTTCCCGAGTCAATAAGTCAGTTAACAAAACTCGAGCGTTTA
GATTTGGGCGATAATGAAATAGAAGAATTGCCGCCACATTTGGGTGATTTACCATCACTG
CAAGAACTATGGCTCGATCATAATCAATTGCAGCGACTGCCGCCCGAAATTGGTAAACTA
AAGAATCTTATGTGTTTGGATGTGTCAGAAAATCGTCTTGAAGATTTACCTGAAGAAATT
GGAGGCTTAGAAAATCTTACTGATTTGCACTTGTCACAAAATCTTCTTGAATTTATACCA
AATGGTATTGAGAAGTTGACTAAATTGACAATATTAAAGTTGGACCAAAATCGCTTGCAT
GTTCTTAATGAAAGCATTGGAATGTGTGAAAATATGCAAGAGCTTATTCTAACTGAGAAC
TTTCTTATCGAATTGCCAAGCTCAATTGGGCGGATGTCGAAATTGAATAATTTAAATGTC
GATAGGAATTCACTCGTATCGGTGCCGTCGGAAATTGGCAATTTGACCAATTTAGGTGTG
CTGAGTTTGCGGGACAATAAATTATCGAAATTGCCATCCGAGCTTGGCAATTGTGGTGCA
CTACATGTTCTCGATGTGTCGGGCAATCGACTTCAATATTTGCCATATTCGTTAGTTAAT
TTACAACTTAAAGCTGTTTGGTTGTCAGAAAATCAAGCGCAGCCATTGTTGACTTTTCAA
CCTGATACTGATGAAGCAACGGGCGAGCAG

>g11970.t9 Gene=g11970 Length=410
MFKCIPIFKGCNRQVEFVDKRHCSLPNVPEEILRYSRSLEELLLDANHIRDLPKNFFRLH
RLRKLGLSDNEIHKLPPDIQNFENLVELDVSRNDIPDIPDDIRHLRLLQIADFSSNPIPK
LPAGFSQLKSLTILGLNDMSLTSLPADFGCLTQLESLELRENLLKNLPESISQLTKLERL
DLGDNEIEELPPHLGDLPSLQELWLDHNQLQRLPPEIGKLKNLMCLDVSENRLEDLPEEI
GGLENLTDLHLSQNLLEFIPNGIEKLTKLTILKLDQNRLHVLNESIGMCENMQELILTEN
FLIELPSSIGRMSKLNNLNVDRNSLVSVPSEIGNLTNLGVLSLRDNKLSKLPSELGNCGA
LHVLDVSGNRLQYLPYSLVNLQLKAVWLSENQAQPLLTFQPDTDEATGEQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
38 g11970.t9 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 2 116 0.000e+00
36 g11970.t9 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 117 212 0.000e+00
37 g11970.t9 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 213 402 0.000e+00
4 g11970.t9 PANTHER PTHR23119:SF44 PROTEIN SCRIBBLE HOMOLOG 1 410 0.000e+00
5 g11970.t9 PANTHER PTHR23119 DISCS LARGE 1 410 0.000e+00
1 g11970.t9 Pfam PF13855 Leucine rich repeat 37 95 0.000e+00
3 g11970.t9 Pfam PF13855 Leucine rich repeat 198 256 0.000e+00
2 g11970.t9 Pfam PF13855 Leucine rich repeat 314 371 7.000e-07
40 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 38 59 6.942e+00
41 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 61 82 6.888e+00
49 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 84 105 7.596e+00
44 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 107 129 4.932e+00
46 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 130 151 4.932e+00
50 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 153 174 6.957e+00
51 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 176 198 7.712e+00
53 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 199 220 7.812e+00
48 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 222 243 6.888e+00
42 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 245 267 7.150e+00
47 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 268 289 5.887e+00
52 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 291 312 4.986e+00
39 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 314 335 5.741e+00
45 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 337 358 7.096e+00
43 g11970.t9 ProSiteProfiles PS51450 Leucine-rich repeat profile. 360 382 6.326e+00
15 g11970.t9 SMART SM00364 LRR_bac_2 36 55 8.500e+01
16 g11970.t9 SMART SM00369 LRR_typ_2 37 58 9.200e+01
23 g11970.t9 SMART SM00369 LRR_typ_2 59 81 2.200e+00
35 g11970.t9 SMART SM00365 LRR_sd22_2 59 84 1.300e+02
25 g11970.t9 SMART SM00369 LRR_typ_2 82 104 1.700e+01
26 g11970.t9 SMART SM00369 LRR_typ_2 105 127 2.500e+02
28 g11970.t9 SMART SM00369 LRR_typ_2 128 150 4.100e+01
10 g11970.t9 SMART SM00364 LRR_bac_2 151 170 4.800e+01
20 g11970.t9 SMART SM00369 LRR_typ_2 151 173 1.400e+01
32 g11970.t9 SMART SM00365 LRR_sd22_2 151 173 9.400e+01
9 g11970.t9 SMART SM00364 LRR_bac_2 174 193 2.300e+02
18 g11970.t9 SMART SM00369 LRR_typ_2 174 196 2.600e-01
31 g11970.t9 SMART SM00365 LRR_sd22_2 174 192 1.400e+01
13 g11970.t9 SMART SM00364 LRR_bac_2 197 216 1.200e+02
17 g11970.t9 SMART SM00369 LRR_typ_2 197 219 7.000e-03
33 g11970.t9 SMART SM00365 LRR_sd22_2 197 225 3.000e+02
11 g11970.t9 SMART SM00364 LRR_bac_2 220 239 2.500e+01
22 g11970.t9 SMART SM00369 LRR_typ_2 220 242 6.700e+00
21 g11970.t9 SMART SM00369 LRR_typ_2 243 265 1.700e+00
34 g11970.t9 SMART SM00365 LRR_sd22_2 243 265 3.200e+02
19 g11970.t9 SMART SM00369 LRR_typ_2 266 289 9.300e+00
8 g11970.t9 SMART SM00364 LRR_bac_2 289 308 2.700e+02
14 g11970.t9 SMART SM00364 LRR_bac_2 312 331 1.300e+02
27 g11970.t9 SMART SM00369 LRR_typ_2 312 334 7.900e+01
29 g11970.t9 SMART SM00369 LRR_typ_2 335 358 1.600e-02
30 g11970.t9 SMART SM00365 LRR_sd22_2 335 357 1.100e+02
12 g11970.t9 SMART SM00364 LRR_bac_2 358 377 2.100e+02
24 g11970.t9 SMART SM00369 LRR_typ_2 359 381 1.200e+02
6 g11970.t9 SUPERFAMILY SSF52058 L domain-like 10 146 0.000e+00
7 g11970.t9 SUPERFAMILY SSF52058 L domain-like 98 392 0.000e+00

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. There were no conditions that were differentially expressed