Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein serrate.

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_3 g1187 g1187.t1 isoform g1187.t1 8597169 8621284
chr_3 g1187 g1187.t1 exon g1187.t1.exon1 8597169 8597963
chr_3 g1187 g1187.t1 cds g1187.t1.CDS1 8597169 8597963
chr_3 g1187 g1187.t1 exon g1187.t1.exon2 8598238 8598815
chr_3 g1187 g1187.t1 cds g1187.t1.CDS2 8598238 8598815
chr_3 g1187 g1187.t1 exon g1187.t1.exon3 8598986 8599480
chr_3 g1187 g1187.t1 cds g1187.t1.CDS3 8598986 8599480
chr_3 g1187 g1187.t1 exon g1187.t1.exon4 8599650 8600042
chr_3 g1187 g1187.t1 cds g1187.t1.CDS4 8599650 8600042
chr_3 g1187 g1187.t1 exon g1187.t1.exon5 8603773 8603913
chr_3 g1187 g1187.t1 cds g1187.t1.CDS5 8603773 8603913
chr_3 g1187 g1187.t1 exon g1187.t1.exon6 8603982 8604281
chr_3 g1187 g1187.t1 cds g1187.t1.CDS6 8603982 8604281
chr_3 g1187 g1187.t1 exon g1187.t1.exon7 8604407 8604464
chr_3 g1187 g1187.t1 cds g1187.t1.CDS7 8604407 8604464
chr_3 g1187 g1187.t1 exon g1187.t1.exon8 8605031 8605321
chr_3 g1187 g1187.t1 cds g1187.t1.CDS8 8605031 8605321
chr_3 g1187 g1187.t1 exon g1187.t1.exon9 8621207 8621284
chr_3 g1187 g1187.t1 cds g1187.t1.CDS9 8621207 8621284
chr_3 g1187 g1187.t1 TSS g1187.t1 NA NA
chr_3 g1187 g1187.t1 TTS g1187.t1 NA NA

Sequences

>g1187.t1 Gene=g1187 Length=3129
ATGAGAATGGAAAGTCTACATACATGGATTCGATTTGGAATATTCATACTCATAGTGATT
GGTGATCTCGTTCCAAATATAAACGGCGCTGGCTCCTTTGAACTAAAAATTCTGGAAATC
TCGAATCCCAACAATCATCTTATAGATGGATATTGCTGTGGTACTAATGAAAAAGAGAAA
TCAAAGACTGAAAATTGTCGCGAATGTGCGACAGCATTTCGATTATGTCTTAAAGAGTTT
CCAAGTGGAACTGAATCGCTGGGATGTCCATTCGGTCAAAGCTCGACAACGATTCTTGGA
GGCTCTAACTTTGAACTTCATGACCAAAAATTTGCCACTATCTCAGTGCCATTCACATTT
CGTTGGACCCAATCATTTTCGTTAATTCTTCAAGCATTGGACATGTACAGAAATTCATCG
TCACCAGCCATTATTGAGGAAGTGGCATATTCGGGAACAATTTCACCACCATCCGATTGG
ATAGTTTTAGATAATAGTAATCAATTGAGCAAGAATGCTCGTATTAAATATAAAATTCGT
GTGATATGTGATAAAAATTATTATAATTCAACATGCACCGTACTGTGTAAGCCTAGAAAT
GACCAATTTGGTCACTATACATGTAACAATAAAGGTCAAAAAATATGTCTCAAAGGCTGG
AGTGGAGAGACATGTGATAAACCAATATGTCCGGAAGGATGTGTGAATGGAATGTGCAAG
AGTCCAGGTGTATGCGAATGTAGACATGGTTATGAAGGCCCGAGCTGCAATCAATGTCTC
ACATATCCTGGCTGTAAAAATGGCTTCTGCACGAGGCCATGGGAGTGCATTTGTAATACA
AATTGGGGTGGGATTTTATGCGATAATGATTTAAATTATTGCGGCACTCATACGCCTTGT
ATGTATGGCGGAACTTGTCATCATTTGGGCGGCGAAAAATTCAATTGTAGCTGTCCAGAA
GGACTTTCTGGGATGCGCTGTGAAATTATTGAGGATCCATGTGCAACAACACCATGTCAA
AATGGTGCAACTTGTATTGTTAAAGACCCCTCAGCAATAAGACGAGGCAGCAATGTCAAT
ACAACGAGACGGCCTGAAGCTCGCTATTATCGTGGCAGCAGCAGTATGGGTGCACCCGTT
TCCGTGCGACCACTTGATCAAAAAACCACAATTGCAGCTCAACAGCAGCAACAACAAGAA
AATGTTACAAACTACGTGTGCAAATGCGCTTCAGGCTATAGTGGTTCACAATGTGAACAA
AATATTGATGAATGCGAAAGTTCGCCTTGCAAAAACGGCGCCACTTGCGTCGATCTGGTG
AACAATTACGAATGCAATTGTGTTCCCGGCTTTAGCGGACCAAATTGCGAGATAGACATT
GACGAGTGTGCCAACGCGCCGTGTCAGAATGGAGGCAAATGCATTGACAAGATCAACGAG
TTTCATTGTGATTGCGAACCTGGCTACAATGGTACGCTATGTGAAATTGATATTAACGAG
TGCCGTTCGAAAAATTGCAACAATAAAACAACTGATTTATGTGCATCGAGTCCATGCAAG
AATAATGGTACATGTGAATTGGGTGACACATGGTATCGTTGTACGTGTGCGCCTGGTTTT
GATGGACCAAACTGTGAGATAAACATTAACGAATGTGCATCACAGCCTTGCGCACAGGGC
TCAACATGCATCGATGATATAGCGAAATTTCGATGCATTTGTCCGCCCAATAAGCGAGGC
AAAAGATGTGAGATCTTGCTTTTAAATGCACCGACTAAAGTGCAGCGTTCCATCGAAAAT
GTTGTCGTCGACGAGTCGAATTTGTGTAATTCCTGCATAATTGGTGAGCATAATGAGATA
CAATGTTCGAATCTATGGTGTGGCTTACCAAATTGTATAAGTGGAAGTGGCAGTAGTGTC
AGCACAAGCAGTATGAGAGCACGACGCGAGATAGGAAGTTGGACGAAGGGACGTGAATGT
AATACAAATGAAGTGTGTGTGCCGGCACTTAAAGAAACTTGCCTCTCACCGCCCTGTATT
AATCGCGGTGATTGTCGAGTACTCGAACAGTCACTACGAACGGCACCACCAAAATATCCC
ACGTCCAACAAATGCTGGCCAAATCAAGCCATTTTAAGCGAAAATTGTTCGCGTATCAAC
ATAATACTAGACATACTTAACATTTCAAAGGGATTATCAACAGAAAGTTACTGTCATAAT
TTGAGAACGCTCTTGGGCGGACGAATGTTGGAACAGAAATTATTTTCCCATTCAGCAATC
ATTTTAATCTGTGATATAAAATCGGGAACAAACGATACAATTGAAGTGACTGTGTCATCA
GATGATGAGTCGTTCACGATTCTGCAAAAAGTCGTTGCAATGTTGGGCGAACTACTTTCA
CGACAGAAGCTGCATGTAAAAGAATCTTGCTTAAGCGACGACTATCCTGAGATAAGTGCA
CTCAATGCAATAATCGAAATCAAAGTAGAGACAGCAATAATTAATGAGAATATCAATAGC
GATGTATATTTGCTCATAGTTTTCGTAGGAATATTACTATTAATCATAAGTTCAATCTCG
TACATCGTTTGTCTTTGGTATTCGAATCATCCGATTTGTTCCCGTCAATCAGAAATAGAT
CTTTCAGTGACTGATACCACCCGTTGTCACGATGAAGAAAAATCAAATAATCTGCAAAAC
GAAGAAAATTTTCGACGCTATGCAAATCCATTAAAGAATTCAAGTTGCTCGCTGCGCAGC
TCTAACGTCGAATTAAATCCTATACATGATCTAGCCGGCCCAAGTGGTCTCAATCGATCG
CAATTATCGATCTTTAAATCACCAAAAGATTTTTCCAATGATTTTGAAACGACAAAGGCA
CATACATTCAATACACCTTCGTCAATGTACTTGAAAACACAGAATTTTGATGTAGATAAA
AATACAATTGAGAGTCAGCAAACCAATAAGGACTTTGAAAAGCGTCTCAATAAAATTGAC
TTCAAGTGCTTTCCTACGACAAACATTACATCAACACCACCAGTGCACCATAATTACAAT
AGCAGTAGCAACATTATTCATCAAACAACTATAAATAATTCAAACGATACGCTCACATTG
CATATATAA

>g1187.t1 Gene=g1187 Length=1042
MRMESLHTWIRFGIFILIVIGDLVPNINGAGSFELKILEISNPNNHLIDGYCCGTNEKEK
SKTENCRECATAFRLCLKEFPSGTESLGCPFGQSSTTILGGSNFELHDQKFATISVPFTF
RWTQSFSLILQALDMYRNSSSPAIIEEVAYSGTISPPSDWIVLDNSNQLSKNARIKYKIR
VICDKNYYNSTCTVLCKPRNDQFGHYTCNNKGQKICLKGWSGETCDKPICPEGCVNGMCK
SPGVCECRHGYEGPSCNQCLTYPGCKNGFCTRPWECICNTNWGGILCDNDLNYCGTHTPC
MYGGTCHHLGGEKFNCSCPEGLSGMRCEIIEDPCATTPCQNGATCIVKDPSAIRRGSNVN
TTRRPEARYYRGSSSMGAPVSVRPLDQKTTIAAQQQQQQENVTNYVCKCASGYSGSQCEQ
NIDECESSPCKNGATCVDLVNNYECNCVPGFSGPNCEIDIDECANAPCQNGGKCIDKINE
FHCDCEPGYNGTLCEIDINECRSKNCNNKTTDLCASSPCKNNGTCELGDTWYRCTCAPGF
DGPNCEININECASQPCAQGSTCIDDIAKFRCICPPNKRGKRCEILLLNAPTKVQRSIEN
VVVDESNLCNSCIIGEHNEIQCSNLWCGLPNCISGSGSSVSTSSMRARREIGSWTKGREC
NTNEVCVPALKETCLSPPCINRGDCRVLEQSLRTAPPKYPTSNKCWPNQAILSENCSRIN
IILDILNISKGLSTESYCHNLRTLLGGRMLEQKLFSHSAIILICDIKSGTNDTIEVTVSS
DDESFTILQKVVAMLGELLSRQKLHVKESCLSDDYPEISALNAIIEIKVETAIINENINS
DVYLLIVFVGILLLIISSISYIVCLWYSNHPICSRQSEIDLSVTDTTRCHDEEKSNNLQN
EENFRRYANPLKNSSCSLRSSNVELNPIHDLAGPSGLNRSQLSIFKSPKDFSNDFETTKA
HTFNTPSSMYLKTQNFDVDKNTIESQQTNKDFEKRLNKIDFKCFPTTNITSTPPVHHNYN
SSSNIIHQTTINNSNDTLTLHI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
45 g1187.t1 CDD cd00054 EGF_CA 290 328 8.03084E-5
47 g1187.t1 CDD cd00054 EGF_CA 421 457 7.35277E-10
44 g1187.t1 CDD cd00054 EGF_CA 459 495 1.45586E-8
43 g1187.t1 CDD cd00054 EGF_CA 497 546 1.00506E-6
46 g1187.t1 CDD cd00054 EGF_CA 548 584 5.65511E-6
28 g1187.t1 Gene3D G3DSA:2.60.40.3510 - 30 183 6.7E-39
29 g1187.t1 Gene3D G3DSA:2.10.25.140 - 184 229 1.4E-19
31 g1187.t1 Gene3D G3DSA:2.10.25.10 Laminin 230 291 3.7E-18
32 g1187.t1 Gene3D G3DSA:2.10.25.10 Laminin 292 330 1.4E-6
30 g1187.t1 Gene3D G3DSA:2.10.25.10 Laminin 422 461 2.4E-17
35 g1187.t1 Gene3D G3DSA:2.10.25.10 Laminin 462 511 1.0E-15
34 g1187.t1 Gene3D G3DSA:2.10.25.10 Laminin 512 550 1.1E-12
33 g1187.t1 Gene3D G3DSA:2.10.25.10 Laminin 551 586 4.6E-12
7 g1187.t1 PANTHER PTHR24044 NOTCH LIGAND FAMILY MEMBER 22 449 4.6E-226
10 g1187.t1 PANTHER PTHR24044:SF456 PROTEIN SERRATE 22 449 4.6E-226
9 g1187.t1 PANTHER PTHR24044 NOTCH LIGAND FAMILY MEMBER 430 508 4.6E-226
12 g1187.t1 PANTHER PTHR24044:SF456 PROTEIN SERRATE 430 508 4.6E-226
8 g1187.t1 PANTHER PTHR24044 NOTCH LIGAND FAMILY MEMBER 514 895 4.6E-226
11 g1187.t1 PANTHER PTHR24044:SF456 PROTEIN SERRATE 514 895 4.6E-226
19 g1187.t1 PRINTS PR00010 Type II EGF-like signature 421 432 2.1E-6
18 g1187.t1 PRINTS PR00010 Type II EGF-like signature 433 440 2.1E-6
21 g1187.t1 PRINTS PR00010 Type II EGF-like signature 441 451 2.1E-6
20 g1187.t1 PRINTS PR00010 Type II EGF-like signature 452 458 2.1E-6
17 g1187.t1 PRINTS PR02059 Jagged/Serrate protein family signature 672 687 5.4E-22
13 g1187.t1 PRINTS PR02059 Jagged/Serrate protein family signature 716 731 5.4E-22
14 g1187.t1 PRINTS PR02059 Jagged/Serrate protein family signature 731 753 5.4E-22
16 g1187.t1 PRINTS PR02059 Jagged/Serrate protein family signature 760 779 5.4E-22
15 g1187.t1 PRINTS PR02059 Jagged/Serrate protein family signature 816 833 5.4E-22
6 g1187.t1 Pfam PF07657 N terminus of Notch ligand 30 104 1.1E-17
5 g1187.t1 Pfam PF01414 Delta serrate ligand 166 225 1.9E-23
2 g1187.t1 Pfam PF00008 EGF-like domain 425 455 1.1E-7
1 g1187.t1 Pfam PF00008 EGF-like domain 463 491 1.8E-7
3 g1187.t1 Pfam PF00008 EGF-like domain 514 544 1.4E-5
4 g1187.t1 Pfam PF12661 Human growth factor-like EGF 557 576 0.021
38 g1187.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 29 -
39 g1187.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 11 -
40 g1187.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 12 20 -
42 g1187.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 21 29 -
37 g1187.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 841 -
41 g1187.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 842 867 -
36 g1187.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 868 1042 -
68 g1187.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 245 256 -
72 g1187.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 316 327 -
74 g1187.t1 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 421 445 -
76 g1187.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 436 447 -
65 g1187.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 445 456 -
70 g1187.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 445 456 -
75 g1187.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 474 485 -
66 g1187.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 483 494 -
71 g1187.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 483 494 -
64 g1187.t1 ProSitePatterns PS01186 EGF-like domain signature 2. 534 545 -
69 g1187.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 534 545 -
73 g1187.t1 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 548 572 -
77 g1187.t1 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 563 574 -
67 g1187.t1 ProSitePatterns PS00022 EGF-like domain signature 1. 572 583 -
78 g1187.t1 ProSiteProfiles PS51051 DSL domain profile. 181 225 15.025
81 g1187.t1 ProSiteProfiles PS50026 EGF-like domain profile. 226 257 7.737
80 g1187.t1 ProSiteProfiles PS50026 EGF-like domain profile. 290 328 18.516
84 g1187.t1 ProSiteProfiles PS50026 EGF-like domain profile. 421 457 25.242
79 g1187.t1 ProSiteProfiles PS50026 EGF-like domain profile. 459 495 23.944
83 g1187.t1 ProSiteProfiles PS50026 EGF-like domain profile. 510 546 20.16
82 g1187.t1 ProSiteProfiles PS50026 EGF-like domain profile. 548 584 19.988
50 g1187.t1 SMART SM00051 dsl11 160 225 1.7E-23
57 g1187.t1 SMART SM00181 egf_5 229 257 18.0
56 g1187.t1 SMART SM00181 egf_5 258 288 19.0
53 g1187.t1 SMART SM00179 egfca_6 290 328 0.0017
58 g1187.t1 SMART SM00181 egf_5 293 328 0.029
59 g1187.t1 SMART SM00181 egf_5 333 419 1.2E-4
55 g1187.t1 SMART SM00179 egfca_6 421 457 2.5E-12
61 g1187.t1 SMART SM00181 egf_5 424 457 2.9E-8
52 g1187.t1 SMART SM00179 egfca_6 459 495 2.2E-11
62 g1187.t1 SMART SM00181 egf_5 462 495 4.4E-7
51 g1187.t1 SMART SM00179 egfca_6 497 546 2.6E-4
60 g1187.t1 SMART SM00181 egf_5 513 546 6.2E-7
54 g1187.t1 SMART SM00179 egfca_6 548 584 4.4E-9
63 g1187.t1 SMART SM00181 egf_5 551 584 7.3E-6
25 g1187.t1 SUPERFAMILY SSF57196 EGF/Laminin 293 329 3.89E-5
24 g1187.t1 SUPERFAMILY SSF57196 EGF/Laminin 421 464 5.47E-13
23 g1187.t1 SUPERFAMILY SSF57196 EGF/Laminin 459 502 4.02E-12
22 g1187.t1 SUPERFAMILY SSF57196 EGF/Laminin 511 552 7.75E-10
26 g1187.t1 SUPERFAMILY SSF57196 EGF/Laminin 548 585 2.0E-9
27 g1187.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
48 g1187.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
49 g1187.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 843 865 -

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:0005112 Notch binding MF
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