Gene loci information

Transcript annotation

  • This transcript has been annotated as Very low-density lipoprotein receptor.

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.t2 isoform g10914.t2 12607114 12643690
chr_1 g10914 g10914.t2 exon g10914.t2.exon1 12607114 12607423
chr_1 g10914 g10914.t2 cds g10914.t2.CDS1 12607114 12607423
chr_1 g10914 g10914.t2 exon g10914.t2.exon2 12620248 12620382
chr_1 g10914 g10914.t2 cds g10914.t2.CDS2 12620248 12620382
chr_1 g10914 g10914.t2 exon g10914.t2.exon3 12624625 12624687
chr_1 g10914 g10914.t2 cds g10914.t2.CDS3 12624625 12624687
chr_1 g10914 g10914.t2 exon g10914.t2.exon4 12630141 12630260
chr_1 g10914 g10914.t2 cds g10914.t2.CDS4 12630141 12630260
chr_1 g10914 g10914.t2 exon g10914.t2.exon5 12632257 12632379
chr_1 g10914 g10914.t2 cds g10914.t2.CDS5 12632257 12632379
chr_1 g10914 g10914.t2 exon g10914.t2.exon6 12636086 12636312
chr_1 g10914 g10914.t2 cds g10914.t2.CDS6 12636086 12636312
chr_1 g10914 g10914.t2 exon g10914.t2.exon7 12636840 12637104
chr_1 g10914 g10914.t2 cds g10914.t2.CDS7 12636840 12637104
chr_1 g10914 g10914.t2 exon g10914.t2.exon8 12637205 12637527
chr_1 g10914 g10914.t2 cds g10914.t2.CDS8 12637205 12637527
chr_1 g10914 g10914.t2 exon g10914.t2.exon9 12637597 12637829
chr_1 g10914 g10914.t2 cds g10914.t2.CDS9 12637597 12637829
chr_1 g10914 g10914.t2 exon g10914.t2.exon10 12637991 12638354
chr_1 g10914 g10914.t2 cds g10914.t2.CDS10 12637991 12638354
chr_1 g10914 g10914.t2 exon g10914.t2.exon11 12638422 12638631
chr_1 g10914 g10914.t2 cds g10914.t2.CDS11 12638422 12638631
chr_1 g10914 g10914.t2 exon g10914.t2.exon12 12638822 12639020
chr_1 g10914 g10914.t2 cds g10914.t2.CDS12 12638822 12639020
chr_1 g10914 g10914.t2 exon g10914.t2.exon13 12639640 12639783
chr_1 g10914 g10914.t2 cds g10914.t2.CDS13 12639640 12639783
chr_1 g10914 g10914.t2 exon g10914.t2.exon14 12643151 12643266
chr_1 g10914 g10914.t2 cds g10914.t2.CDS14 12643151 12643266
chr_1 g10914 g10914.t2 exon g10914.t2.exon15 12643508 12643690
chr_1 g10914 g10914.t2 cds g10914.t2.CDS15 12643508 12643690
chr_1 g10914 g10914.t2 TTS g10914.t2 12644154 12644154
chr_1 g10914 g10914.t2 TSS g10914.t2 NA NA

Sequences

>g10914.t2 Gene=g10914 Length=3015
ATGGTGATCACTGTGTTAAGCGCTAAAAAAGCGAAAATTTTTTGTTTGTTCTGGTTTTTA
TTTATCGTCTCATTTGCAAATGGCCAAAACGATAGCATCAATAATAGCAATGTTCAGCAG
CATCATCAACAACTTTATAAATATAATTCAATCAATAATAGAAGTGTGACAAATGGAGAA
AGTTTAAAAACACCTCCTGCAATTAGTAAAGATAAGCTAGCATCAAAATCAAATATAAAT
AGCAAATATGAAACACAATCTACAGTGACTTCGGCTATTGCTATTGGTCTTTTTCCTGGT
TCTAAAAAAATGCGTCAAAGAAAATGTACAGAACGACAGTTTCAATGTAACAATGGTGAA
TGCATCCCTATGAAATACCTTTGTGATGGTGAACCAGATTGCCAAGATAAAAGTGATGAA
GATCAAACAGAATGTTCTCATAAACTAGCAGTGGTTGCAGTAAATGCTGCTATTCCACAA
TCAGATTTGGATAGGAAAACCATAAAGGAAAACGAATGTAGTCAAGATCAATTTAGATGT
AATAATGGACGATGTATACCAAAAAGATGGACCTGTGATCAGGAGAAAGATTGTAGCGAT
GGATCTGATGAAGATGCAAGCCATTGTCAAATAAAAATGTGTTCGTCCGAGGACTTTACG
TGCAGGAGCAACAATGGTGAATGCATTCCACTTTCGTGGATGTGTGATGGCAACAAAGAT
TGTACAGATGGATCTGATGAAGCATCATGTAACGATACTTGTCGTTCCGATGAGTTTACA
TGTAATAATGGTAGATGTATTCAAAGTCGGTGGGTTTGTGATCGTGACGATGATTGTGGT
GATGGATCTGATGAAGCCAAGTGTACTCCTACGAAATGTGATCCAATTAAACAATTTCAA
TGCTCAGAGAAGTATTGTATTACATCGAAATGGCGTTGTGACGGCGAACAAGATTGTCCT
GATGGTTCCGATGAAAAAGATTGTTCGATTATAATTCGACGTGAATCCTCATGTGTACAA
GCAGAGTATCAATGTAAAGATGGTATAACATGCATTCATCGTTCATGGGTTTGTGATGGT
GAGAAAGATTGCCCAGGAGGCGATGACGAGCAACCACCGCTCTGCCAAAATGTCACATGT
CGAGCAGATCAATTTCAATGTGCAGATAAGACATGCATTCATGGTCGTTTCCACTGTTCA
GGCAAAGCTGAATGTAAGGATGGAAGTGATGAACTAAATTGCCCTGTTCCAAAGAAATCA
TGTGATCGCAAAACGGAATTTGATTGTGGTGATGGAATGTGCATACCTCTTTCAAAAGTA
TGTGATAAGCACCAAGATTGTCCGGATGCAGAGGACGAACCAGTAGGAAAATGTGGACGT
GATGAATGCAAATCAAATAATGGAGGCTGTTCACAATTATGCGTTGATACGCAAGCCGGC
TACTATTGTGAATGTCGTCAAGGCTATAAATTATCTAGTGACAATCGTACGTGTGAGGAC
ATTAATGAATGTGAAATTCCTGGTTCATGTTCTCAATTATGTACAAATGAACGTGGCGGT
TTTAAATGCGAATGTGTTTCTGGCTTTTTGAGAGATCCTCGAGACCACACTAAATGCAAA
GCCACAGAAGGACATGCATCGTTGCTTTTTGCACGTCGTCATGACATCAGAAAGATTTCA
CTTGACCATCGTGAGATGACTTCAATTGTTAATGAAACAAAGTCGGCTACAGCATTAGAC
TATGTATTCAGAACTGGCATGATATTTTGGAGTGACGTAACGGAACAAAGAATTTATAAA
GCACCAATTGATGAAGGTACAGAGCAAATTGTTGTACTGCAGGATAAGACAGTGACATCA
GATGGACTTGCGGTTGATTGGATTTACAATCACATCTACTTTACTGATACAAAGCGTTAT
ACAATTGAGATAATGAATTTTGACGGAAACATGGGAAAGGTGCTGATTAAAGATAATTTA
GAGATACCACGTGCCATTGCAGTTAATCCTCTCGATGGATGGATGTTCTGGAGTGATTGG
GGTTCAAGTCCAAGAATAGAACGTGCTGGTATGGACGGTACACATCGTCAAACAATCGTC
AGCTATGACGTAAAATGGCCTAACGGATTAACACTTGATCTCGTGCAAAAACGCGTCTAT
TGGGTTGATGCTAAATTAAATGTAATTTCATCATGTAATTTCGATGGCTCTGGTCGTAAT
TTAGTGCTTCATTCAACCGATTCACTTCGACATCCATTTTCAATTACAACATTCGAGGAT
TATGTATATTGGACGGACTGGGATAAAGAGGCGGTTTTCCGTGCAAATAAATTCAATGGC
AATGATGTTGAACCTGTCACTGCATTACATATGCTTCAACATCCGATGACAATTCATGTA
TATCATCCATACCGACAGCCAGATGGTGAAAATCATTGTCAAGCAGTGAATGGACATTGT
TCACATTTGTGCTTGCCAGCTCCAAGAATCAACGCTCAAAGTGCACGAATCTCGTGTGCC
TGTCCAACAGGATTAAAACTTATGGATGATGGTCTGATGTGTGTTGAAGACGAAACTCAT
ACAACAACAGGAAAAACAGAAACAGCAACGAATCATCATTCGCATCATTTGGAAACAACA
ACAAAAATATCGAAAGGAATTGAACATCATTCGTCCAATATTTATGATAGTGATGTTGAT
GTTATTAAAAGCCACATTGGATTATATAATAATGAAACACAAGCAAGTGTACTAGCTGAC
GGTCCTGACAATGGAATGGTTGCAATCATAACGATTGTTGTAGCCACATTGCTGGTTCTT
GTGCTAACAGTCCTGGCTGTACTCGTCTACCGACATTATGTTCACAAAAATCTAACGTCC
ATAAACTTTGATAATCCTGTGTATCGTAAAACAACGGAGGATCAAGTGCGTTTGAAGAAA
TCGCTTTCGCCTATAATTTATCCAAGCACGGTTGGAGAGGAGTTACGCGCTTTAGCACAA
GATTGTCCGATTTAA

>g10914.t2 Gene=g10914 Length=1004
MVITVLSAKKAKIFCLFWFLFIVSFANGQNDSINNSNVQQHHQQLYKYNSINNRSVTNGE
SLKTPPAISKDKLASKSNINSKYETQSTVTSAIAIGLFPGSKKMRQRKCTERQFQCNNGE
CIPMKYLCDGEPDCQDKSDEDQTECSHKLAVVAVNAAIPQSDLDRKTIKENECSQDQFRC
NNGRCIPKRWTCDQEKDCSDGSDEDASHCQIKMCSSEDFTCRSNNGECIPLSWMCDGNKD
CTDGSDEASCNDTCRSDEFTCNNGRCIQSRWVCDRDDDCGDGSDEAKCTPTKCDPIKQFQ
CSEKYCITSKWRCDGEQDCPDGSDEKDCSIIIRRESSCVQAEYQCKDGITCIHRSWVCDG
EKDCPGGDDEQPPLCQNVTCRADQFQCADKTCIHGRFHCSGKAECKDGSDELNCPVPKKS
CDRKTEFDCGDGMCIPLSKVCDKHQDCPDAEDEPVGKCGRDECKSNNGGCSQLCVDTQAG
YYCECRQGYKLSSDNRTCEDINECEIPGSCSQLCTNERGGFKCECVSGFLRDPRDHTKCK
ATEGHASLLFARRHDIRKISLDHREMTSIVNETKSATALDYVFRTGMIFWSDVTEQRIYK
APIDEGTEQIVVLQDKTVTSDGLAVDWIYNHIYFTDTKRYTIEIMNFDGNMGKVLIKDNL
EIPRAIAVNPLDGWMFWSDWGSSPRIERAGMDGTHRQTIVSYDVKWPNGLTLDLVQKRVY
WVDAKLNVISSCNFDGSGRNLVLHSTDSLRHPFSITTFEDYVYWTDWDKEAVFRANKFNG
NDVEPVTALHMLQHPMTIHVYHPYRQPDGENHCQAVNGHCSHLCLPAPRINAQSARISCA
CPTGLKLMDDGLMCVEDETHTTTGKTETATNHHSHHLETTTKISKGIEHHSSNIYDSDVD
VIKSHIGLYNNETQASVLADGPDNGMVAIITIVVATLLVLVLTVLAVLVYRHYVHKNLTS
INFDNPVYRKTTEDQVRLKKSLSPIIYPSTVGEELRALAQDCPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
60 g10914.t2 CDD cd00112 LDLa 109 141 2.08888E-10
55 g10914.t2 CDD cd00112 LDLa 173 205 2.05938E-11
57 g10914.t2 CDD cd00112 LDLa 214 250 4.56766E-10
58 g10914.t2 CDD cd00112 LDLa 298 328 1.4069E-9
56 g10914.t2 CDD cd00112 LDLa 338 371 3.13301E-7
59 g10914.t2 CDD cd00112 LDLa 380 414 1.33636E-8
54 g10914.t2 CDD cd00112 LDLa 425 453 7.8748E-7
61 g10914.t2 CDD cd00054 EGF_CA 500 529 3.2873E-4
43 g10914.t2 Gene3D G3DSA:4.10.400.10 - 103 148 1.3E-15
42 g10914.t2 Gene3D G3DSA:4.10.400.10 - 167 212 3.7E-15
41 g10914.t2 Gene3D G3DSA:4.10.400.10 - 213 250 2.0E-13
44 g10914.t2 Gene3D G3DSA:4.10.400.10 - 251 293 3.0E-15
40 g10914.t2 Gene3D G3DSA:4.10.400.10 - 294 330 2.3E-12
46 g10914.t2 Gene3D G3DSA:4.10.400.10 - 333 378 5.4E-12
39 g10914.t2 Gene3D G3DSA:4.10.400.10 - 379 417 1.0E-11
45 g10914.t2 Gene3D G3DSA:4.10.400.10 - 418 453 3.9E-10
35 g10914.t2 Gene3D G3DSA:2.10.25.10 Laminin 463 504 4.3E-16
36 g10914.t2 Gene3D G3DSA:2.10.25.10 Laminin 505 542 7.2E-10
38 g10914.t2 Gene3D G3DSA:2.120.10.30 TolB 546 804 8.6E-98
37 g10914.t2 Gene3D G3DSA:2.10.25.10 Laminin 806 856 1.1E-18
16 g10914.t2 PANTHER PTHR24270 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED 29 328 9.7E-234
14 g10914.t2 PANTHER PTHR24270 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED 170 390 9.7E-234
15 g10914.t2 PANTHER PTHR24270 LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED 337 820 9.7E-234
18 g10914.t2 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 183 204 6.3E-49
22 g10914.t2 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 226 247 6.3E-49
20 g10914.t2 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 264 285 6.3E-49
21 g10914.t2 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 304 325 6.3E-49
17 g10914.t2 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 349 370 6.3E-49
19 g10914.t2 PRINTS PR00261 Low density lipoprotein (LDL) receptor signature 390 411 6.3E-49
1 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 108 145 1.9E-12
3 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 172 209 1.3E-11
5 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 213 250 3.3E-11
8 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 253 288 1.2E-12
4 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 292 328 2.0E-11
7 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 337 371 1.4E-9
2 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 379 414 2.3E-11
6 g10914.t2 Pfam PF00057 Low-density lipoprotein receptor domain class A 420 458 2.2E-7
10 g10914.t2 Pfam PF14670 Coagulation Factor Xa inhibitory site 463 498 6.7E-13
9 g10914.t2 Pfam PF07645 Calcium-binding EGF domain 500 539 2.2E-6
13 g10914.t2 Pfam PF00058 Low-density lipoprotein receptor repeat class B 675 713 1.5E-11
12 g10914.t2 Pfam PF00058 Low-density lipoprotein receptor repeat class B 718 756 2.6E-4
11 g10914.t2 Pfam PF14670 Coagulation Factor Xa inhibitory site 813 854 3.0E-9
49 g10914.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 28 -
50 g10914.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 12 -
51 g10914.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 13 23 -
53 g10914.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 24 28 -
48 g10914.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 925 -
52 g10914.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 926 950 -
47 g10914.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 951 1004 -
87 g10914.t2 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 185 209 -
86 g10914.t2 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 228 250 -
90 g10914.t2 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 266 288 -
89 g10914.t2 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 306 328 -
88 g10914.t2 ProSitePatterns PS01209 LDL-receptor class A (LDLRA) domain signature. 434 458 -
92 g10914.t2 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 474 485 -
85 g10914.t2 ProSitePatterns PS01186 EGF-like domain signature 2. 483 498 -
91 g10914.t2 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 500 523 -
99 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 108 146 14.05
98 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 172 210 14.35
100 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 213 251 14.55
102 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 253 289 14.6
103 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 292 329 13.887
104 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 337 376 11.7
101 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 379 415 12.463
105 g10914.t2 ProSiteProfiles PS50068 LDL-receptor class A (LDLRA) domain profile. 420 459 12.262
94 g10914.t2 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 586 629 11.85
97 g10914.t2 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 630 672 12.871
96 g10914.t2 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 673 716 15.354
93 g10914.t2 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 717 761 12.43
95 g10914.t2 ProSiteProfiles PS51120 LDL-receptor class B (LDLRB) repeat profile. 762 804 6.536
68 g10914.t2 SMART SM00192 LDLa_2 108 147 1.2E-14
67 g10914.t2 SMART SM00192 LDLa_2 172 211 1.8E-14
79 g10914.t2 SMART SM00181 egf_5 172 210 35.0
69 g10914.t2 SMART SM00192 LDLa_2 213 252 4.6E-13
82 g10914.t2 SMART SM00181 egf_5 213 251 150.0
64 g10914.t2 SMART SM00192 LDLa_2 253 290 4.7E-16
84 g10914.t2 SMART SM00181 egf_5 253 289 240.0
70 g10914.t2 SMART SM00192 LDLa_2 292 330 1.7E-11
71 g10914.t2 SMART SM00192 LDLa_2 337 377 8.6E-11
66 g10914.t2 SMART SM00192 LDLa_2 379 416 6.4E-12
65 g10914.t2 SMART SM00192 LDLa_2 420 460 8.8E-10
72 g10914.t2 SMART SM00179 egfca_6 459 499 4.0E-4
80 g10914.t2 SMART SM00181 egf_5 462 499 3.5E-5
73 g10914.t2 SMART SM00179 egfca_6 500 540 2.0E-7
83 g10914.t2 SMART SM00181 egf_5 503 540 0.29
75 g10914.t2 SMART SM00135 LY_2 566 608 4.1
74 g10914.t2 SMART SM00135 LY_2 610 652 3.5E-8
77 g10914.t2 SMART SM00135 LY_2 653 696 1.1E-14
76 g10914.t2 SMART SM00135 LY_2 697 739 8.5E-15
78 g10914.t2 SMART SM00135 LY_2 741 783 6.9E-6
81 g10914.t2 SMART SM00181 egf_5 812 855 7.2
30 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 106 143 4.71E-11
27 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 172 209 8.12E-11
28 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 206 250 2.88E-10
25 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 253 291 1.14E-10
31 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 292 329 2.36E-10
24 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 336 374 2.23E-8
29 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 374 415 5.11E-10
26 g10914.t2 SUPERFAMILY SSF57424 LDL receptor-like module 421 454 8.25E-8
32 g10914.t2 SUPERFAMILY SSF57184 Growth factor receptor domain 460 856 1.33E-19
23 g10914.t2 SUPERFAMILY SSF63825 YWTD domain 548 808 1.7E-51
34 g10914.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 28 -
62 g10914.t2 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 28 -
33 g10914.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 25 -
63 g10914.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 927 949 -

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
GO:0005509 calcium ion 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.

Raw TPM values