Gene loci information

Transcript annotation

  • This transcript has been annotated as Neurogenic locus protein delta.

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 g11501 g11501.t1 isoform g11501.t1 16654158 16667003
chr_1 g11501 g11501.t1 exon g11501.t1.exon1 16654158 16654205
chr_1 g11501 g11501.t1 cds g11501.t1.CDS1 16654158 16654205
chr_1 g11501 g11501.t1 exon g11501.t1.exon2 16659034 16659357
chr_1 g11501 g11501.t1 cds g11501.t1.CDS2 16659034 16659357
chr_1 g11501 g11501.t1 exon g11501.t1.exon3 16661247 16661319
chr_1 g11501 g11501.t1 cds g11501.t1.CDS3 16661247 16661319
chr_1 g11501 g11501.t1 exon g11501.t1.exon4 16664059 16664310
chr_1 g11501 g11501.t1 cds g11501.t1.CDS4 16664059 16664310
chr_1 g11501 g11501.t1 exon g11501.t1.exon5 16664933 16664993
chr_1 g11501 g11501.t1 cds g11501.t1.CDS5 16664933 16664993
chr_1 g11501 g11501.t1 exon g11501.t1.exon6 16665212 16665632
chr_1 g11501 g11501.t1 cds g11501.t1.CDS6 16665212 16665632
chr_1 g11501 g11501.t1 exon g11501.t1.exon7 16665765 16667003
chr_1 g11501 g11501.t1 cds g11501.t1.CDS7 16665765 16667003
chr_1 g11501 g11501.t1 TSS g11501.t1 NA NA
chr_1 g11501 g11501.t1 TTS g11501.t1 NA NA

Sequences

>g11501.t1 Gene=g11501 Length=2418
ATGAATTGGATTTCTTTCTTCATTTGCATTTTTTTGACATTCTCACAGATTACGTGTTCC
GGAATATTTGAACTGAGACTAAAGTCATTTCAAAATGATAAAGGTGAAAATAACTTTAAT
CGATGTTGCACGGAAAAGCAAACACCAACTGGCGCTTGTCAAGGTAGCTGTAAGACGAGA
TTTCGAGTTTGCTTGAAGCAATATCAGGCCGAGATTGATACTACATCGCCATGCACATTT
GGCTCGGCTGCAACATCAATTTTAGGCGAAAATACATTCAATCTCACAAAATTGTCAATG
GTAGCGAGGAAGCAACCACAAGATGATTTATCAACTAATCCAATTAGATTTCCTTTCGAA
TTTACCTGGCCTCGTGCATTTACACTTATTGTTGAAGCCTATCATGACGTATCAAACGAT
GATGGAATATCGAGATCATCAACTGAATCATTGATAGCCCGTTTTTCAATACAAGGTGAA
TTGAGTGTCTCTGCCAATTGGACACAATATTCATCACATAAACAAGCTTCCAAAGAAATC
GAATTCGAATACCGCGTTACTTGTGATTCAAATTATTATGGTGCAGGCTGTGAAACACTT
TGTCGCGAGCGTGACGATAATTTTGGACATTATGCGTGCTCAGCAACTGGTCAACGCATG
TGCCTTTCTGGTTGGCAAGGAGATTATTGCACAAAACCACGTTGTTCTCCCGGGTGCAAT
TTAGAACACGGACACTGTGAAAGGCCAAACGAGTGCACATGCAAGGCCGGATGGAAGGGA
CCAAATTGTGACGAGTGCGAGCTCTATCCAGGCTGCATTCATGGTTATTGTACACAAAAA
TGGGAATGTATTTGCAATGAAGGCTGGGGCGGTCTCTTTTGTAATCAGGACTTGAATTTT
TGTACAAATCATAAACCTTGTCATAATGGTGGAACGTGCACTAATACAGGTCAGGGCTCA
TATACTTGTAAATGCGGACCAGGATACACTGGAGTTGATTGCGAAATTAAAATGAAAGAT
TGTAGCGAGAATCCATGCCTTAATAATGGCACATGCAATGACGATCCTAATGGATACAAA
TGTGAATGCCGATATGGTTGGATTGGTAAACATTGTGAGACTCAAACTGTAACATGCGCT
TCTAAGCCATGTCTGCACGACGGCACTTGTCATAATTCTACGATAGGCGCAAGATGTGAG
TGTGCAATTGGCTATAGTGGACGATATTGTGAAATGCAAGTTCAAAATTGTTTACCAAAT
CCCTGCCAAAATAATGGCAAATGTATGGCTCTAAAAGGCAATAATTATCAATGTCAATGT
GAGAAGGGTTTTAAAGGCTTATTGTGTGAGGAAAATATTGATGATTGTGCCGGCAACCCT
TGCAAGAATGGTGGCACATGCATTGATGGCATCAATCAATATCAATGCAAATGCCAGTCT
GGCTATACGGGCGTTAATTGCGAAAAACGAGTTGACTTCTGTCGAACGAAACCTTGTGCG
AATGGCGGCACATGTATTGAAGAGGGCAATAGTTTTAAATGTCTTTGCCGAAACGGTTTC
GAAGGTAACGATTGCAGCCAAGACATTGATGAGTGCTTATCATCACCATGCAAGAACGGT
GCATCATGCATAAATCGAGTCAACTCTTATGAATGCAAATGCAGTGACAACTTTCAAGGA
GTTAATTGCGACATACCCGTATCATTTAAATTGGAGAATCAAGCGTCAACGTCGACTTAT
CAAGAAGCACAGATCTCAAAAGAGCACATGAGTTCGACTAAAGTTGCACTCATTGCTTTT
GCATCAGTTGCTGTTCCGTTTGTAGCAATCTGCGGTATCGCTGTTGTCATTTGTATGAAA
AGAAAAAGAAAAAGAGAGCAAGAGAAAGATGATGCAGAAGCACGTAAACAAAATGAACAA
AATGCTTCTCATATCACACACTTACACCAGCATCATCATAATTCAATAGTGGCCATTAAA
CGAACATCTAATAGTAATATGGCACTCGATTCCTCAACTCATCATATGATCAAAAATACA
TGGGATAAGAGTGTCAACAATATGTCGCATTCAGCAGCCACTATTGATGATGGATGCATG
AATGTATATGGAGCAATGTCAAATTTTGTTGATCATGCAGGATCCAATACAAATCAACTT
TTAAATTCTAGTGATAGTTATCAATCTCAAATATTGCCTCAAACACTTCAGCGCGCAAAA
AGTCAAAAGCAGCTGAACACTGATCCGGCAGTTGTAAATCGTGCATCGATAATCATGCAT
CGGCATCATCAGCAACAACAGCCAAAAAAAGAATTAGCGCTCGATAACAGAATATCGTTA
CTAGATGAATCGTGGAGCGGGAATAATAATGCCAGCACTAGTCGACAAATGGATAGATGT
AGTCCTCAGCATATATAA

>g11501.t1 Gene=g11501 Length=805
MNWISFFICIFLTFSQITCSGIFELRLKSFQNDKGENNFNRCCTEKQTPTGACQGSCKTR
FRVCLKQYQAEIDTTSPCTFGSAATSILGENTFNLTKLSMVARKQPQDDLSTNPIRFPFE
FTWPRAFTLIVEAYHDVSNDDGISRSSTESLIARFSIQGELSVSANWTQYSSHKQASKEI
EFEYRVTCDSNYYGAGCETLCRERDDNFGHYACSATGQRMCLSGWQGDYCTKPRCSPGCN
LEHGHCERPNECTCKAGWKGPNCDECELYPGCIHGYCTQKWECICNEGWGGLFCNQDLNF
CTNHKPCHNGGTCTNTGQGSYTCKCGPGYTGVDCEIKMKDCSENPCLNNGTCNDDPNGYK
CECRYGWIGKHCETQTVTCASKPCLHDGTCHNSTIGARCECAIGYSGRYCEMQVQNCLPN
PCQNNGKCMALKGNNYQCQCEKGFKGLLCEENIDDCAGNPCKNGGTCIDGINQYQCKCQS
GYTGVNCEKRVDFCRTKPCANGGTCIEEGNSFKCLCRNGFEGNDCSQDIDECLSSPCKNG
ASCINRVNSYECKCSDNFQGVNCDIPVSFKLENQASTSTYQEAQISKEHMSSTKVALIAF
ASVAVPFVAICGIAVVICMKRKRKREQEKDDAEARKQNEQNASHITHLHQHHHNSIVAIK
RTSNSNMALDSSTHHMIKNTWDKSVNNMSHSAATIDDGCMNVYGAMSNFVDHAGSNTNQL
LNSSDSYQSQILPQTLQRAKSQKQLNTDPAVVNRASIIMHRHHQQQQPKKELALDNRISL
LDESWSGNNNASTSRQMDRCSPQHI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
44 g11501.t1 CDD cd00054 EGF_CA 297 335 1.33046E-8
41 g11501.t1 CDD cd00054 EGF_CA 342 373 7.18668E-7
47 g11501.t1 CDD cd00054 EGF_CA 379 411 5.00111E-4
46 g11501.t1 CDD cd00054 EGF_CA 419 450 0.00543406
43 g11501.t1 CDD cd00054 EGF_CA 452 488 2.94538E-9
42 g11501.t1 CDD cd00054 EGF_CA 491 525 1.23861E-5
45 g11501.t1 CDD cd00054 EGF_CA 528 563 2.37128E-8
33 g11501.t1 Coils Coil Coil 622 642 -
23 g11501.t1 Gene3D G3DSA:2.60.40.3510 - 19 188 2.0E-52
24 g11501.t1 Gene3D G3DSA:2.10.25.140 - 189 233 1.3E-18
26 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 235 297 1.8E-21
31 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 298 338 8.9E-11
32 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 339 377 2.0E-12
25 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 378 416 8.7E-10
30 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 417 454 1.0E-10
29 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 455 492 8.0E-15
28 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 493 528 7.2E-11
27 g11501.t1 Gene3D G3DSA:2.10.25.10 Laminin 529 565 1.1E-13
85 g11501.t1 MobiDBLite mobidb-lite consensus disorder prediction 785 805 -
10 g11501.t1 PANTHER PTHR24044:SF380 DELTA-LIKE PROTEIN 1 10 487 4.6E-185
12 g11501.t1 PANTHER PTHR24044 NOTCH LIGAND FAMILY MEMBER 10 487 4.6E-185
11 g11501.t1 PANTHER PTHR24044:SF380 DELTA-LIKE PROTEIN 1 474 569 4.6E-185
13 g11501.t1 PANTHER PTHR24044 NOTCH LIGAND FAMILY MEMBER 474 569 4.6E-185
14 g11501.t1 PRINTS PR00010 Type II EGF-like signature 452 463 1.1E-6
16 g11501.t1 PRINTS PR00010 Type II EGF-like signature 464 471 1.1E-6
15 g11501.t1 PRINTS PR00010 Type II EGF-like signature 472 482 1.1E-6
17 g11501.t1 PRINTS PR00010 Type II EGF-like signature 483 489 1.1E-6
9 g11501.t1 Pfam PF07657 N terminus of Notch ligand 20 93 7.1E-26
8 g11501.t1 Pfam PF01414 Delta serrate ligand 167 230 2.8E-22
5 g11501.t1 Pfam PF00008 EGF-like domain 301 331 2.0E-6
7 g11501.t1 Pfam PF00008 EGF-like domain 341 371 3.3E-7
4 g11501.t1 Pfam PF00008 EGF-like domain 379 409 4.1E-6
2 g11501.t1 Pfam PF00008 EGF-like domain 417 446 1.4E-8
1 g11501.t1 Pfam PF00008 EGF-like domain 456 485 2.0E-8
3 g11501.t1 Pfam PF00008 EGF-like domain 494 523 1.2E-5
6 g11501.t1 Pfam PF00008 EGF-like domain 532 561 8.7E-6
36 g11501.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
37 g11501.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
38 g11501.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
40 g11501.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
35 g11501.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 594 -
39 g11501.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 595 619 -
34 g11501.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 620 805 -
77 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 252 263 -
69 g11501.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 323 334 -
75 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 323 334 -
82 g11501.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 352 363 -
70 g11501.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 361 372 -
76 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 361 372 -
67 g11501.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 399 410 -
78 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 399 410 -
71 g11501.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 438 449 -
79 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 438 449 -
81 g11501.t1 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 452 476 -
84 g11501.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 467 478 -
66 g11501.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 476 487 -
72 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 476 487 -
68 g11501.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 514 525 -
73 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 514 525 -
80 g11501.t1 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 521 552 -
83 g11501.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 543 554 -
74 g11501.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 552 563 -
86 g11501.t1 ProSiteProfiles PS51051 DSL domain profile. 186 230 15.485
91 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 231 264 8.397
88 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 297 335 24.258
93 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 337 373 21.186
94 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 375 411 17.45
90 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 413 450 19.018
92 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 452 488 25.407
89 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 490 526 19.154
87 g11501.t1 ProSiteProfiles PS50026 EGF-like domain profile. 528 564 21.745
49 g11501.t1 SMART SM00051 dsl11 167 230 3.1E-25
63 g11501.t1 SMART SM00181 egf_5 234 264 19.0
60 g11501.t1 SMART SM00181 egf_5 265 295 0.49
54 g11501.t1 SMART SM00179 egfca_6 297 335 2.7E-9
61 g11501.t1 SMART SM00181 egf_5 300 335 4.1E-7
55 g11501.t1 SMART SM00179 egfca_6 337 373 4.9E-4
62 g11501.t1 SMART SM00181 egf_5 340 373 1.3E-6
64 g11501.t1 SMART SM00181 egf_5 378 411 2.2E-5
56 g11501.t1 SMART SM00179 egfca_6 379 411 0.02
51 g11501.t1 SMART SM00179 egfca_6 413 450 0.011
57 g11501.t1 SMART SM00181 egf_5 416 450 2.1E-5
53 g11501.t1 SMART SM00179 egfca_6 452 488 5.1E-11
58 g11501.t1 SMART SM00181 egf_5 455 488 8.4E-8
50 g11501.t1 SMART SM00179 egfca_6 490 526 6.6E-5
65 g11501.t1 SMART SM00181 egf_5 493 526 2.3E-6
52 g11501.t1 SMART SM00179 egfca_6 528 564 8.4E-12
59 g11501.t1 SMART SM00181 egf_5 531 564 9.8E-7
20 g11501.t1 SUPERFAMILY SSF57196 EGF/Laminin 300 337 2.29E-7
21 g11501.t1 SUPERFAMILY SSF57196 EGF/Laminin 337 375 1.0E-8
19 g11501.t1 SUPERFAMILY SSF57196 EGF/Laminin 377 414 7.63E-8
18 g11501.t1 SUPERFAMILY SSF57184 Growth factor receptor domain 439 564 2.67E-13
22 g11501.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 20 -
48 g11501.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 595 617 -

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:0016020 membrane CC
GO:0007275 multicellular organism development BP
GO:0005509 calcium ion binding MF
GO:0016021 integral component of membrane CC
GO:0007154 cell communication BP
GO:0007219 Notch signaling pathway BP

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