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 g10914 g10914.t3 isoform g10914.t3 12607114 12630666
chr_1 g10914 g10914.t3 exon g10914.t3.exon1 12607114 12607423
chr_1 g10914 g10914.t3 cds g10914.t3.CDS1 12607114 12607423
chr_1 g10914 g10914.t3 exon g10914.t3.exon2 12620248 12620382
chr_1 g10914 g10914.t3 cds g10914.t3.CDS2 12620248 12620382
chr_1 g10914 g10914.t3 exon g10914.t3.exon3 12630141 12630260
chr_1 g10914 g10914.t3 cds g10914.t3.CDS3 12630141 12630260
chr_1 g10914 g10914.t3 exon g10914.t3.exon4 12630521 12630666
chr_1 g10914 g10914.t3 cds g10914.t3.CDS4 12630521 12630666
chr_1 g10914 g10914.t3 TSS g10914.t3 NA NA
chr_1 g10914 g10914.t3 TTS g10914.t3 NA NA

Sequences

>g10914.t3 Gene=g10914 Length=711
ATGGTGATCACTGTGTTAAGCGCTAAAAAAGCGAAAATTTTTTGTTTGTTCTGGTTTTTA
TTTATCGTCTCATTTGCAAATGGCCAAAACGATAGCATCAATAATAGCAATGTTCAGCAG
CATCATCAACAACTTTATAAATATAATTCAATCAATAATAGAAGTGTGACAAATGGAGAA
AGTTTAAAAACACCTCCTGCAATTAGTAAAGATAAGCTAGCATCAAAATCAAATATAAAT
AGCAAATATGAAACACAATCTACAGTGACTTCGGCTATTGCTATTGGTCTTTTTCCTGGT
TCTAAAAAAATGCGTCAAAGAAAATGTACAGAACGACAGTTTCAATGTAACAATGGTGAA
TGCATCCCTATGAAATACCTTTGTGATGGTGAACCAGATTGCCAAGATAAAAGTGATGAA
GATCAAACAGAATGTTCTCATAAACAAAACGAATGTAGTCAAGATCAATTTAGATGTAAT
AATGGACGATGTATACCAAAAAGATGGACCTGTGATCAGGAGAAAGATTGTAGCGATGGA
TCTGATGAAGATGCAAGCCATTGTCAACAACCGTCACACTGTCCCAATAATGAATTTCTG
TGTCACAATGGTGAACAGTGTATACCCAGAGATTGGGTTTGTGATAATGCAATAGACTGT
TCAGATAAATCCGACGAAAAATCATGTGTTGGTAAGCTTTTGACAGTTTAA

>g10914.t3 Gene=g10914 Length=236
MVITVLSAKKAKIFCLFWFLFIVSFANGQNDSINNSNVQQHHQQLYKYNSINNRSVTNGE
SLKTPPAISKDKLASKSNINSKYETQSTVTSAIAIGLFPGSKKMRQRKCTERQFQCNNGE
CIPMKYLCDGEPDCQDKSDEDQTECSHKQNECSQDQFRCNNGRCIPKRWTCDQEKDCSDG
SDEDASHCQQPSHCPNNEFLCHNGEQCIPRDWVCDNAIDCSDKSDEKSCVGKLLTV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g10914.t3 CDD cd00112 LDLa 109 141 1.77648E-10
22 g10914.t3 CDD cd00112 LDLa 152 184 1.72534E-11
21 g10914.t3 CDD cd00112 LDLa 194 229 1.69775E-9
13 g10914.t3 Gene3D G3DSA:4.10.400.10 - 103 147 4.7E-16
15 g10914.t3 Gene3D G3DSA:4.10.400.10 - 148 191 4.4E-16
14 g10914.t3 Gene3D G3DSA:4.10.400.10 - 192 232 4.8E-13
4 g10914.t3 PANTHER PTHR24270 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED 28 229 1.0E-42
6 g10914.t3 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 119 140 3.4E-24
5 g10914.t3 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 162 183 3.4E-24
7 g10914.t3 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 205 226 3.4E-24
1 g10914.t3 Pfam PF00057 Low-density lipoprotein receptor domain class A 108 145 2.9E-13
2 g10914.t3 Pfam PF00057 Low-density lipoprotein receptor domain class A 151 188 2.0E-12
3 g10914.t3 Pfam PF00057 Low-density lipoprotein receptor domain class A 193 229 5.5E-12
17 g10914.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 28 -
18 g10914.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 12 -
19 g10914.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 13 23 -
20 g10914.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 24 28 -
16 g10914.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 236 -
29 g10914.t3 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 164 188 -
28 g10914.t3 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 207 229 -
30 g10914.t3 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 108 146 14.05
31 g10914.t3 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 151 189 14.35
32 g10914.t3 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 193 230 13.113
27 g10914.t3 SMART SM00192 LDLa_2 108 147 1.2E-14
25 g10914.t3 SMART SM00192 LDLa_2 151 190 1.5E-14
26 g10914.t3 SMART SM00192 LDLa_2 193 231 2.7E-12
10 g10914.t3 SUPERFAMILY SSF57424 LDL receptor-like module 106 143 1.7E-11
9 g10914.t3 SUPERFAMILY SSF57424 LDL receptor-like module 150 188 1.7E-11
8 g10914.t3 SUPERFAMILY SSF57424 LDL receptor-like module 192 230 4.45E-11
12 g10914.t3 SignalP_EUK SignalP-noTM SignalP-noTM 1 28 -
24 g10914.t3 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 28 -
11 g10914.t3 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 25 -

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