Gene loci information

Transcript annotation

  • This transcript has been annotated as Low-density lipoprotein receptor-related protein 6.

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 g2360 g2360.t3 isoform g2360.t3 17183243 17184858
chr_3 g2360 g2360.t3 exon g2360.t3.exon1 17183243 17183892
chr_3 g2360 g2360.t3 cds g2360.t3.CDS1 17183479 17183892
chr_3 g2360 g2360.t3 exon g2360.t3.exon2 17184005 17184858
chr_3 g2360 g2360.t3 cds g2360.t3.CDS2 17184005 17184856
chr_3 g2360 g2360.t3 TSS g2360.t3 NA NA
chr_3 g2360 g2360.t3 TTS g2360.t3 NA NA

Sequences

>g2360.t3 Gene=g2360 Length=1504
ATGCTGGGCAACCGATAACATTACGAAACTCACCTACTTCACATGCATCCTCAATATCAA
CGACGTCGTCGTCATCATCAACCCTTCTCATATTCACAACATATCACGATATTCGCATAG
CGAATTTGTCACGTAATCATGTCACCAGCATTACAACAATTACAAAGGACTTGGTTGAAG
GAGCGGGTCTCGACTTTTATTATGACAAGCAATTGGTATGTTGGACGGATCAGGGAATGG
AAGCAATTCAATGTAAAAAAATGAATGCATCATTTTATGGTGATCATCAGCCCGTTGGAC
CGGTGGGAATTGACGAGTTGACAGAAAACATTGACAAGATTAGCATAATTACCAAACGAA
TTGAGAAACCTGAGGGAATCGCAATTGATTGGTATACAGACAAAATTTACTGGGTTGATG
GTGAACTTAATAATATTGAAGTGACAACATTAAATGGAAAATATCGCAAGTTGCTTTTCT
GGACAGATCTCGATCAGCCAAGGGCAATTTCACTTGTGCCCGCGCAGAAGCTAATGATAT
GGTGTGACTGGGGAGAAATTCCTCGAATTGAACGAGCCTCGATGGACGGGGATAAGTATA
GTCGCATGATTCTCGTTAGCGATCGTATTTATTGGCCAAATGGACTCACGGTTGATATTG
AAAACAACTTAATCTACTGGGTTGATGGGAAACTTCAATTTCTTGATGTAATGAATCTTG
ACGGCAGTGGACGACGTACGATATTGAAAGACTTGAATTATCCATATAGTGTCACGTACA
TAAATCGAATGCTCTTTTGGAGCGATTGGAATGTGGGAAAAATAAATTCCTATGATCTTT
CAACGGGTGAGCAGAAGGAGGTCATTGATGACTCTGAAGTTCCAATCACAGTTCATGCAT
GGCATCAAGTACTTCAACCATCAGCGCCTAATCCATGCAAAATCAACAATGGAAATTGCT
CACATTTGTGTCTGCTGTCATCAACAAATATAAAAGGCTTCTCATGTGCATGTCCGACAG
GTGTAAAATTGCTTACAGATACACTGTGTGCAGACGGACCTCAAAATGTCATTTTTCTTG
TTCAACGTACGCAAATAAGCAGAATAAGCTTAGACTCACCTGACTATACGAGTTTTCCAC
TCTCGCTTGGCAGAGTTCGTTCAGCAATTTCAATTGATTATGATCCAGTTGACGATTTTA
TTTACTGGTCAGATGAAGATCAACGAGTAATTAAGAAATCACGACAAGACGGGACACTTA
TTACTGATGTAATTAATACAGAAATCAAACACCCTGATGGACTCGCAATTGATTGGATTG
CGAGAAACTTGCTTTGGACAGATTCCGGATCTGATCGCATTGAAGTTTCTCGATTGAATG
GACTTTATAGAAGAGTTTTAATCAATGACAATCTCGATGAGCCTCGAGGCATTGCTGTTG
CACCAACTTTAGGCTGGATGTTTTGGGGCGATTGGGGAAAAAAGCCAAAAATTGAACGAG
CTTC

>g2360.t3 Gene=g2360 Length=422
MEAIQCKKMNASFYGDHQPVGPVGIDELTENIDKISIITKRIEKPEGIAIDWYTDKIYWV
DGELNNIEVTTLNGKYRKLLFWTDLDQPRAISLVPAQKLMIWCDWGEIPRIERASMDGDK
YSRMILVSDRIYWPNGLTVDIENNLIYWVDGKLQFLDVMNLDGSGRRTILKDLNYPYSVT
YINRMLFWSDWNVGKINSYDLSTGEQKEVIDDSEVPITVHAWHQVLQPSAPNPCKINNGN
CSHLCLLSSTNIKGFSCACPTGVKLLTDTLCADGPQNVIFLVQRTQISRISLDSPDYTSF
PLSLGRVRSAISIDYDPVDDFIYWSDEDQRVIKKSRQDGTLITDVINTEIKHPDGLAIDW
IARNLLWTDSGSDRIEVSRLNGLYRRVLINDNLDEPRGIAVAPTLGWMFWGDWGKKPKIE
RA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g2360.t3 Gene3D G3DSA:2.120.10.30 TolB 25 270 0.0000000
17 g2360.t3 Gene3D G3DSA:2.120.10.30 TolB 271 422 0.0000000
6 g2360.t3 PANTHER PTHR24270:SF12 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6 37 422 0.0000000
7 g2360.t3 PANTHER PTHR24270 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED 37 422 0.0000000
3 g2360.t3 Pfam PF00058 Low-density lipoprotein receptor repeat class B 55 91 0.0000038
5 g2360.t3 Pfam PF00058 Low-density lipoprotein receptor repeat class B 102 141 0.0000001
1 g2360.t3 Pfam PF14670 Coagulation Factor Xa inhibitory site 234 268 0.0000000
4 g2360.t3 Pfam PF00058 Low-density lipoprotein receptor repeat class B 321 360 0.0000760
2 g2360.t3 Pfam PF00058 Low-density lipoprotein receptor repeat class B 364 401 0.0000000
21 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 10 54 5.4220000
23 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 55 97 13.2890000
22 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 98 143 12.5000000
24 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 144 185 11.1770000
20 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 320 362 14.3790000
19 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 363 405 14.6110000
25 g2360.t3 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 406 422 7.8590000
16 g2360.t3 SMART SM00135 LY_2 35 77 0.0000000
11 g2360.t3 SMART SM00135 LY_2 78 121 0.0007600
15 g2360.t3 SMART SM00135 LY_2 124 166 0.0000000
13 g2360.t3 SMART SM00135 LY_2 167 206 0.4900000
14 g2360.t3 SMART SM00135 LY_2 300 342 0.1000000
12 g2360.t3 SMART SM00135 LY_2 343 385 0.0000000
10 g2360.t3 SMART SM00135 LY_2 386 422 0.0006200
9 g2360.t3 SUPERFAMILY SSF63825 YWTD domain 35 227 0.0000000
8 g2360.t3 SUPERFAMILY SSF63825 YWTD domain 280 421 0.0000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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