Gene loci information

Transcript annotation

  • This transcript has been annotated as Low-density lipoprotein receptor-related protein 8.

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 g10914 g10914.t6 isoform g10914.t6 12637205 12638631
chr_1 g10914 g10914.t6 exon g10914.t6.exon1 12637205 12637527
chr_1 g10914 g10914.t6 cds g10914.t6.CDS1 12637258 12637527
chr_1 g10914 g10914.t6 exon g10914.t6.exon2 12637597 12637829
chr_1 g10914 g10914.t6 cds g10914.t6.CDS2 12637597 12637829
chr_1 g10914 g10914.t6 exon g10914.t6.exon3 12637991 12638354
chr_1 g10914 g10914.t6 cds g10914.t6.CDS3 12637991 12638354
chr_1 g10914 g10914.t6 exon g10914.t6.exon4 12638422 12638631
chr_1 g10914 g10914.t6 cds g10914.t6.CDS4 12638422 12638631
chr_1 g10914 g10914.t6 TSS g10914.t6 NA NA
chr_1 g10914 g10914.t6 TTS g10914.t6 NA NA

Sequences

>g10914.t6 Gene=g10914 Length=1130
CTGTTCCAAAGAAATCATGTGATCGCAAAACGGAATTTGATTGTGGTGATGGAATGTGCA
TACCTCTTTCAAAAGTATGTGATAAGCACCAAGATTGTCCGGATGCAGAGGACGAACCAG
TAGGAAAATGTGGACGTGATGAATGCAAATCAAATAATGGAGGCTGTTCACAATTATGCG
TTGATACGCAAGCCGGCTACTATTGTGAATGTCGTCAAGGCTATAAATTATCTAGTGACA
ATCGTACGTGTGAGGACATTAATGAATGTGAAATTCCTGGTTCATGTTCTCAATTATGTA
CAAATGAACGTGGCGGTTTTAAATGCGAATGTGTTTCTGGCTTTTTGAGAGATCCTCGAG
ACCACACTAAATGCAAAGCCACAGAAGGACATGCATCGTTGCTTTTTGCACGTCGTCATG
ACATCAGAAAGATTTCACTTGACCATCGTGAGATGACTTCAATTGTTAATGAAACAAAGT
CGGCTACAGCATTAGACTATGTATTCAGAACTGGCATGATATTTTGGAGTGACGTAACGG
AACAAAGAATTTATAAAGCACCAATTGATGAAGGTACAGAGCAAATTGTTGTACTGCAGG
ATAAGACAGTGACATCAGATGGACTTGCGGTTGATTGGATTTACAATCACATCTACTTTA
CTGATACAAAGCGTTATACAATTGAGATAATGAATTTTGACGGAAACATGGGAAAGGTGC
TGATTAAAGATAATTTAGAGATACCACGTGCCATTGCAGTTAATCCTCTCGATGGATGGA
TGTTCTGGAGTGATTGGGGTTCAAGTCCAAGAATAGAACGTGCTGGTATGGACGGTACAC
ATCGTCAAACAATCGTCAGCTATGACGTAAAATGGCCTAACGGATTAACACTTGATCTCG
TGCAAAAACGCGTCTATTGGGTTGATGCTAAATTAAATGTAATTTCATCATGTAATTTCG
ATGGCTCTGGTCGTAATTTAGTGCTTCATTCAACCGATTCACTTCGACATCCATTTTCAA
TTACAACATTCGAGGATTATGTATATTGGACGGACTGGGATAAAGAGGCGGTTTTCCGTG
CAAATAAATTCAATGGCAATGATGTTGAACCTGTCACTGCATTACATATG

>g10914.t6 Gene=g10914 Length=359
MCIPLSKVCDKHQDCPDAEDEPVGKCGRDECKSNNGGCSQLCVDTQAGYYCECRQGYKLS
SDNRTCEDINECEIPGSCSQLCTNERGGFKCECVSGFLRDPRDHTKCKATEGHASLLFAR
RHDIRKISLDHREMTSIVNETKSATALDYVFRTGMIFWSDVTEQRIYKAPIDEGTEQIVV
LQDKTVTSDGLAVDWIYNHIYFTDTKRYTIEIMNFDGNMGKVLIKDNLEIPRAIAVNPLD
GWMFWSDWGSSPRIERAGMDGTHRQTIVSYDVKWPNGLTLDLVQKRVYWVDAKLNVISSC
NFDGSGRNLVLHSTDSLRHPFSITTFEDYVYWTDWDKEAVFRANKFNGNDVEPVTALHM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g10914.t6 CDD cd00112 LDLa 2 21 1.07046E-4
16 g10914.t6 CDD cd00054 EGF_CA 68 97 8.30187E-6
14 g10914.t6 Gene3D G3DSA:4.10.400.10 - 1 28 1.4E-6
12 g10914.t6 Gene3D G3DSA:2.10.25.10 Laminin 31 72 1.2E-16
11 g10914.t6 Gene3D G3DSA:2.10.25.10 Laminin 73 110 2.0E-10
13 g10914.t6 Gene3D G3DSA:2.120.10.30 TolB 114 358 1.3E-95
5 g10914.t6 PANTHER PTHR24270:SF3 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 8 2 352 6.4E-119
6 g10914.t6 PANTHER PTHR24270 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED 2 352 6.4E-119
2 g10914.t6 Pfam PF14670 Coagulation Factor Xa inhibitory site 31 66 1.9E-13
1 g10914.t6 Pfam PF07645 Calcium-binding EGF domain 68 107 6.2E-7
4 g10914.t6 Pfam PF00058 Low-density lipoprotein receptor repeat class B 243 281 4.1E-12
3 g10914.t6 Pfam PF00058 Low-density lipoprotein receptor repeat class B 286 324 7.2E-5
19 g10914.t6 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 42 53 -
17 g10914.t6 ProSitePatterns PS01186 EGF-like domain signature 2. 51 66 -
18 g10914.t6 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 68 91 -
31 g10914.t6 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 154 197 11.85
32 g10914.t6 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 198 240 12.871
33 g10914.t6 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 241 284 15.354
29 g10914.t6 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 285 329 12.43
30 g10914.t6 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 330 359 5.863
20 g10914.t6 SMART SM00179 egfca_6 27 67 4.0E-4
28 g10914.t6 SMART SM00181 egf_5 30 67 3.5E-5
21 g10914.t6 SMART SM00179 egfca_6 68 108 2.0E-7
27 g10914.t6 SMART SM00181 egf_5 71 108 0.29
26 g10914.t6 SMART SM00135 LY_2 134 176 4.1
22 g10914.t6 SMART SM00135 LY_2 178 220 3.5E-8
23 g10914.t6 SMART SM00135 LY_2 221 264 1.1E-14
25 g10914.t6 SMART SM00135 LY_2 265 307 8.5E-15
24 g10914.t6 SMART SM00135 LY_2 309 351 6.9E-6
8 g10914.t6 SUPERFAMILY SSF57424 LDL receptor-like module 1 22 5.24E-5
9 g10914.t6 SUPERFAMILY SSF57196 EGF/Laminin 31 75 9.21E-12
10 g10914.t6 SUPERFAMILY SSF57196 EGF/Laminin 68 105 1.01E-7
7 g10914.t6 SUPERFAMILY SSF63825 YWTD domain 116 352 6.67E-50

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF
GO:0005509 calcium ion 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