Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Low-density lipoprotein receptor-related protein 2.

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 g13804 g13804.t3 isoform g13804.t3 32485195 32491933
chr_1 g13804 g13804.t3 exon g13804.t3.exon1 32485195 32485305
chr_1 g13804 g13804.t3 cds g13804.t3.CDS1 32485304 32485305
chr_1 g13804 g13804.t3 exon g13804.t3.exon2 32491193 32491519
chr_1 g13804 g13804.t3 cds g13804.t3.CDS2 32491193 32491519
chr_1 g13804 g13804.t3 exon g13804.t3.exon3 32491585 32491933
chr_1 g13804 g13804.t3 cds g13804.t3.CDS3 32491585 32491678
chr_1 g13804 g13804.t3 TSS g13804.t3 NA NA
chr_1 g13804 g13804.t3 TTS g13804.t3 NA NA

Sequences

>g13804.t3 Gene=g13804 Length=787
GGTAAGAAAAAAAATTTAATTTTTTGTATGAAATATTAAAGAAATATTTTATTTTAATAG
TGATAATGATTGCGGTGATAATTCTGATGAAGATGCTATCCATTGTGCTCAAAGAACTTG
TCCACAAAATTCATTCAGATGTCCAAATCATCGTTGTATTCCAGCTACATGGTAAGAATA
AATATTTTAGGAAATTTTCTAGTTACTAATTTTAATTTTAATTTAGGTATTGTGATGGTG
ATGACGATTGCGGTGATGGAGCTGATGAACCACCAGAATATTGCAAATCTGAAGGAAGAA
CATGCTTTGGTGATCTTTTCACTTGTGATAATGGCAATTGCATTCCTAGGCGATGGTGAT
AATGATTGTCTCGATAACAGCGATGAAGATAATAGACATCAATGCAATGATAGAAAATGT
GATCCAGAAACTGAATTTACTTGTGAAGAGAACAAACAATGGGGCAGATCACAATGTATA
CCCAAGAAATGGCTTTGTGATGGCGATCCTGATTGCGTTGATGGTGCTGATGAAAATACA
ACCCTTCACAATTGTCCAACTCCTCAACCTTGCTCAGAAGATCAATTTACGTGTGAGAAT
GGAAGATGTATCAATAAAGGATGGCTTTGTGATCATGATAATGATTGTGGTGATGGCTCA
GATGAAGGCAAATTCTAAAAATGTTATTAAAAATTACGTAAATTTATTCAGAAATTGACT
GAAAAATATTTGTATAATCTAAATATTTCTATCCTGAATGATGCAGTATTTTCTCTTTTG
TGTAATA

>g13804.t3 Gene=g13804 Length=140
MELMNHQNIANLKEEHALVIFSLVIMAIAFLGDGDNDCLDNSDEDNRHQCNDRKCDPETE
FTCEENKQWGRSQCIPKKWLCDGDPDCVDGADENTTLHNCPTPQPCSEDQFTCENGRCIN
KGWLCDHDNDCGDGSDEGKF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g13804.t3 CDD cd00112 LDLa 57 94 2.04689E-5
15 g13804.t3 CDD cd00112 LDLa 106 137 4.22035E-10
10 g13804.t3 Gene3D G3DSA:4.10.400.10 - 51 102 6.2E-13
11 g13804.t3 Gene3D G3DSA:4.10.400.10 - 103 140 5.8E-16
3 g13804.t3 PANTHER PTHR22722:SF9 LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2A-RELATED 27 138 5.2E-27
4 g13804.t3 PANTHER PTHR22722 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 2-RELATED 27 138 5.2E-27
5 g13804.t3 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 23 44 1.8E-20
7 g13804.t3 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 72 93 1.8E-20
6 g13804.t3 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 116 137 1.8E-20
2 g13804.t3 Pfam PF00057 Low-density lipoprotein receptor domain class A 54 98 3.0E-9
1 g13804.t3 Pfam PF00057 Low-density lipoprotein receptor domain class A 105 137 6.5E-12
12 g13804.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 15 -
14 g13804.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 16 32 -
13 g13804.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 33 140 -
20 g13804.t3 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 54 101 13.075
19 g13804.t3 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 105 137 12.562
17 g13804.t3 SMART SM00192 LDLa_2 54 102 2.3E-10
18 g13804.t3 SMART SM00192 LDLa_2 105 139 1.0E-10
8 g13804.t3 SUPERFAMILY SSF57424 LDL receptor-like module 55 96 9.95E-8
9 g13804.t3 SUPERFAMILY SSF57424 LDL receptor-like module 103 138 2.36E-12

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