Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Leucine-rich repeat-containing protein 15.

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_4 g16491 g16491.t2 TSS g16491.t2 9689178 9689178
chr_4 g16491 g16491.t2 isoform g16491.t2 9689202 9691109
chr_4 g16491 g16491.t2 exon g16491.t2.exon1 9689202 9690531
chr_4 g16491 g16491.t2 cds g16491.t2.CDS1 9689202 9690531
chr_4 g16491 g16491.t2 exon g16491.t2.exon2 9690743 9691109
chr_4 g16491 g16491.t2 cds g16491.t2.CDS2 9690743 9691107
chr_4 g16491 g16491.t2 TTS g16491.t2 9691332 9691332

Sequences

>g16491.t2 Gene=g16491 Length=1697
ATGAAGTTGATATTTCTATTTTTATCATATTTTATTTCATACACTGTTGCACAACAAGCA
ATTTGTGAATTTGGAATAAGAAATGTTGGTGGTGTTATAGGTTATTCTTGTGGTTTATCA
GTGAACAATCCTGAAGGTCAAACAATTACAGAAATTGGAGGTATTCATTTAGAAGGTTAC
ACTGATGCTGATGTACAAGGAATTTTGCGTATTAACGGTTCAATTGAGACAGCTTTTCCT
GCAATTTTCTGTCAACGATTTCCAAATATTCAAAGAGCTTTAGTTCATGGTTTAAATATC
ACTGAAATTACAGATAATTCATTTTCCACGTGTACTTCACTCGACTGGCTTTATATTTTA
TCGAATAGAATCAGTTCAATTAGTCAAAATGCTTTTGCCAATAATCAAAATTTGATTCAT
ATTGATTTGGACAATAATTTATTATCGACTTTACCTGAAAATGTTTTTGGAACTTTGAGT
AATTTAGAAATTCTTGACTTAAGAAATAATCCATTTGTTGAAATTCCATCTGGTGCTTTT
AATGGATTGAGTTCTTTACAAATTCTGTATATGCAAAACACAAGACTTACAGCCATAAAT
CCAGCTTGGTTTTCGTCAACATCAAATTTAGAAACTTTATATTTGACAAATAATCAAATC
AGTCAAATTTCTCCAAATACTTTTAATAATTTACAAAATTTGATATCACTAAATCTAAAT
GGCAACAACATTGGAGCTTTTCAAGCTGAAACATTTTCTGGCTTAAGAAATCTTCAATCT
CTTTCTGTTGGTGGCAATAACATCAGTGAAATTAATAAAAATTCTTTTGTTGGCCTTGAA
AATCTTTTGACGCTTGATTTAAGTGGAAATTTCTTTTCAATCATTAGAAATGGAACTTTT
AGAGCTTTGACAAATCTTCGATCACTTTTATTGAGTAATTCAAGAATTAATGACTTTGAA
ATTGATGCTTTTGATGGACTAACAAATTTAACAATTCTGAATTTGAATTTTAATTTACTC
GAGGATTTGCCAGCATCAGTTTTTGCTCCTTTAAGAAATTTAGAATATTGTGGTCTTTGG
AGCAACAGAATAAAAACATTCAGAAGAAATGTTTTTGGAACTGACTTGTCAACTCTTTTG
ACTTTAGATTTGGATGAAAATGTTGTTAATGCACTTGAAAGAAGTGTTTTTTATGATGCA
ACAAATTTGAATCGATTTTTATTTAGTAGCAATTTTTGTGGGAATGGAATTTTCAATGGA
TTTGCACAAAATAGAGCGGAATTTATGCAGAGACTTGAACGATGCTTCAGAAACTTTGAG
TTAATTATTGATACCGTAACTGATAACAATGTCGATTATCTTTTCTTCCGTGGTGAAAAT
CCTGGAATTGTTGCTCGAGTGCAAGCTGAAGATGAAATTCAAATTGCATTGACACCATTC
AATTTTCCATGGTCACCAATGATTGAGGTCATCATTGGAGCAGCAAACAATACACGATCA
ATCATCAGACGAAATCAAGATGAAGATGTGGCTGTTGTGCCATCACCAGGAATCATCAGG
AGAAATCAACAAAATTTATTCAGAATAGTTTGGGCAAATCATGTGATTTTGGTGTTTAGA
GAGAATGAACAATGGCCATTTTTGGTTCACACAATGATTGACTTTTTTAATGTCAATTTC
TATGGATTGAGAACTTT

>g16491.t2 Gene=g16491 Length=565
MKLIFLFLSYFISYTVAQQAICEFGIRNVGGVIGYSCGLSVNNPEGQTITEIGGIHLEGY
TDADVQGILRINGSIETAFPAIFCQRFPNIQRALVHGLNITEITDNSFSTCTSLDWLYIL
SNRISSISQNAFANNQNLIHIDLDNNLLSTLPENVFGTLSNLEILDLRNNPFVEIPSGAF
NGLSSLQILYMQNTRLTAINPAWFSSTSNLETLYLTNNQISQISPNTFNNLQNLISLNLN
GNNIGAFQAETFSGLRNLQSLSVGGNNISEINKNSFVGLENLLTLDLSGNFFSIIRNGTF
RALTNLRSLLLSNSRINDFEIDAFDGLTNLTILNLNFNLLEDLPASVFAPLRNLEYCGLW
SNRIKTFRRNVFGTDLSTLLTLDLDENVVNALERSVFYDATNLNRFLFSSNFCGNGIFNG
FAQNRAEFMQRLERCFRNFELIIDTVTDNNVDYLFFRGENPGIVARVQAEDEIQIALTPF
NFPWSPMIEVIIGAANNTRSIIRRNQDEDVAVVPSPGIIRRNQQNLFRIVWANHVILVFR
ENEQWPFLVHTMIDFFNVNFYGLRT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g16491.t2 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 55 206 1.6E-31
20 g16491.t2 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 207 289 1.6E-20
18 g16491.t2 Gene3D G3DSA:3.80.10.10 Ribonuclease Inhibitor 290 434 4.2E-21
7 g16491.t2 PANTHER PTHR46473:SF8 ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY 97 146 1.8E-89
10 g16491.t2 PANTHER PTHR46473:SF8 ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY 97 234 1.8E-89
12 g16491.t2 PANTHER PTHR46473 GH08155P 97 146 1.8E-89
15 g16491.t2 PANTHER PTHR46473 GH08155P 97 234 1.8E-89
9 g16491.t2 PANTHER PTHR46473:SF8 ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY 140 290 1.8E-89
14 g16491.t2 PANTHER PTHR46473 GH08155P 140 290 1.8E-89
8 g16491.t2 PANTHER PTHR46473:SF8 ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY 208 330 1.8E-89
13 g16491.t2 PANTHER PTHR46473 GH08155P 208 330 1.8E-89
6 g16491.t2 PANTHER PTHR46473:SF8 ELRR (EXTRACELLULAR LEUCINE-RICH REPEAT) ONLY 284 411 1.8E-89
11 g16491.t2 PANTHER PTHR46473 GH08155P 284 411 1.8E-89
1 g16491.t2 Pfam PF13855 Leucine rich repeat 160 220 3.8E-15
4 g16491.t2 Pfam PF00560 Leucine Rich Repeat 233 255 1.5
2 g16491.t2 Pfam PF13855 Leucine rich repeat 256 316 1.9E-12
3 g16491.t2 Pfam PF13306 BspA type Leucine rich repeat region (6 copies) 322 412 0.0027
5 g16491.t2 Pfam PF12248 Farnesoic acid 0-methyl transferase 475 565 2.6E-14
22 g16491.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 17 -
23 g16491.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
24 g16491.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 12 -
25 g16491.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 17 -
21 g16491.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 18 565 -
45 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 113 134 6.588
39 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 137 158 6.603
42 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 161 182 7.204
41 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 185 206 4.547
46 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 209 230 8.528
40 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 233 254 6.026
47 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 257 278 6.934
48 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 281 302 6.11
49 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 305 326 5.64
44 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 329 350 7.419
43 g16491.t2 ProSiteProfiles PS51450 Leucine-rich repeat profile. 378 399 4.747
37 g16491.t2 SMART SM00369 LRR_typ_2 111 134 100.0
32 g16491.t2 SMART SM00369 LRR_typ_2 136 158 8.2
30 g16491.t2 SMART SM00369 LRR_typ_2 159 182 1.3E-4
31 g16491.t2 SMART SM00369 LRR_typ_2 183 206 6.9
29 g16491.t2 SMART SM00369 LRR_typ_2 207 230 0.12
28 g16491.t2 SMART SM00369 LRR_typ_2 231 254 0.7
34 g16491.t2 SMART SM00369 LRR_typ_2 255 278 0.21
35 g16491.t2 SMART SM00369 LRR_typ_2 279 302 0.081
38 g16491.t2 SMART SM00369 LRR_typ_2 303 326 4.7
36 g16491.t2 SMART SM00369 LRR_typ_2 327 350 9.2E-4
33 g16491.t2 SMART SM00369 LRR_typ_2 351 374 82.0
27 g16491.t2 SMART SM00369 LRR_typ_2 376 399 29.0
16 g16491.t2 SUPERFAMILY SSF52058 L domain-like 80 412 1.29E-57
17 g16491.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 17 -
26 g16491.t2 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 17 -

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. There were no conditions that were differentially expressed