Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein crumbs.

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 g10284 g10284.t5 isoform g10284.t5 8628585 8630059
chr_1 g10284 g10284.t5 exon g10284.t5.exon1 8628585 8629452
chr_1 g10284 g10284.t5 TTS g10284.t5 8628629 8628629
chr_1 g10284 g10284.t5 cds g10284.t5.CDS1 8629225 8629452
chr_1 g10284 g10284.t5 exon g10284.t5.exon2 8629518 8630059
chr_1 g10284 g10284.t5 cds g10284.t5.CDS2 8629518 8629904
chr_1 g10284 g10284.t5 TSS g10284.t5 NA NA

Sequences

>g10284.t5 Gene=g10284 Length=1410
ACATCACGACGGGAAATAATTTTACATGCATATGCAAAGAAGGCTTTGAAGGGGCACTTT
GTGACTACGCTTACTGTCTTGTTGAGCCGTGCAAAAATGATGGAAACTGTTATACAGATT
CAGAAGTGCCAGAGTGTAAATGCCAACTTGGTTTCATGGGAAAATATTGTGAAATTGATA
TTGATGATTGTGCCTCAACTCCATGTCAAAATAATGCAACATGCATTGACTTGGTGAACG
ATTATAAATGCGAATGTGAAGGAACTGGTTTCACAGGAGAAAATTGTGAAAATGACATTG
ATGAATGTTTGACAGAAAATATTTCATGTGGCGGTTTGGGAACTTGTATTAATACAAAAG
GATCTTATAAATGTCAATGTAATGAAGGAATGTGTGGATCAGATTGCAATTTAGTAGATC
CTTGTCAAGAAAATGAGTCACCGTGCATGAATGGTGGTAAATGTATTGAAACATGTGTCA
CATTCCCTGACTATAGGTGTCAATGTGTTGATGGTTATGCTGGCAAAAATTGCACAGAAC
AAGTGCTTTTAGCAACAGGACCAACTGCAGGTGACATTTTAATAATTGTCATTCCAATCG
TCGTCAGTTTATTAGCTATCGGTGGAATTGTTCTTGCAGTACTTTTAATGATGGCAAGAA
ATAAAAGAGCAACGAGAGGAACTTATAGTCCTTCAGCGCAAGAATATTGCAATCCTCGAC
TTGAAATGGATTCTGTTTTAAAACAACCACCAGAGGAGAGACTTATCTAAAGAATACTTA
GTAATTTATCAGTAATTAAAATTATGTGAACTGAATGTGCCTTGTGTGAGATTGATATAA
AAATGAATGTCCTTACTCCATCACGTGCGAATGATGTGTTAGTTATTATGTGATATAAAA
AAAAGACAGAAAAAGAAAGAAAAATTTCAAATTTGTACTTAATATTTTTTTACGCCTAGC
AATAAGACGTATGTAGATGTATGAGCCTTTAATGACTTTTTCTCATGTATAGACTAAAAT
TTAAATTTTTAATTATACATGTAAAATAAATTACCTTCTATACATGAACAGTCATTTAGA
CAAAGTATTGAGATTTGTTGATAATTTCAAAAAAACAAAAGCAATGACCGACCGTCCGAT
ATTTTACGATGAAATAAAAGTATGAACAACTAAATCATTCGTTAAGTTAAAGCTAATTAG
TTAGAACACATAGAAATTTAATTAAAAATGATTAAAGAAAGAAACCAATTTTAAGAATAA
TTATGTGGCATTTTTTCGATAATATTGAAATACTTATTATCATAAGAAAAGCTTTATCGA
AGATACATAACTGAAAAGAAGATAATAAAATTTATTAAAAAGATCCAAAACAAGTGAATT
TCTTTCTTAACTCGTACAATCAAATTTGGT

>g10284.t5 Gene=g10284 Length=204
MGKYCEIDIDDCASTPCQNNATCIDLVNDYKCECEGTGFTGENCENDIDECLTENISCGG
LGTCINTKGSYKCQCNEGMCGSDCNLVDPCQENESPCMNGGKCIETCVTFPDYRCQCVDG
YAGKNCTEQVLLATGPTAGDILIIVIPIVVSLLAIGGIVLAVLLMMARNKRATRGTYSPS
AQEYCNPRLEMDSVLKQPPEERLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g10284.t5 CDD cd00054 EGF_CA 8 45 2.29879E-7
22 g10284.t5 CDD cd00054 EGF_CA 47 84 1.62827E-6
20 g10284.t5 CDD cd00054 EGF_CA 87 127 2.75165E-4
14 g10284.t5 Gene3D G3DSA:2.10.25.10 Laminin 1 46 5.2E-15
16 g10284.t5 Gene3D G3DSA:2.10.25.10 Laminin 47 86 1.3E-8
15 g10284.t5 Gene3D G3DSA:2.10.25.10 Laminin 87 130 1.2E-9
4 g10284.t5 PANTHER PTHR24049:SF19 PROTEIN CRUMBS HOMOLOG 2 2 54 7.5E-45
6 g10284.t5 PANTHER PTHR24049 CRUMBS FAMILY MEMBER 2 54 7.5E-45
5 g10284.t5 PANTHER PTHR24049:SF19 PROTEIN CRUMBS HOMOLOG 2 54 204 7.5E-45
7 g10284.t5 PANTHER PTHR24049 CRUMBS FAMILY MEMBER 54 204 7.5E-45
10 g10284.t5 PRINTS PR00010 Type II EGF-like signature 8 19 1.0E-5
9 g10284.t5 PRINTS PR00010 Type II EGF-like signature 100 107 1.0E-5
11 g10284.t5 PRINTS PR00010 Type II EGF-like signature 111 121 1.0E-5
8 g10284.t5 PRINTS PR00010 Type II EGF-like signature 122 128 1.0E-5
1 g10284.t5 Pfam PF00008 EGF-like domain 12 43 2.8E-9
3 g10284.t5 Pfam PF07645 Calcium-binding EGF domain 47 78 8.4E-7
2 g10284.t5 Pfam PF00008 EGF-like domain 90 125 1.6E-7
18 g10284.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 140 -
19 g10284.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 141 164 -
17 g10284.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 165 204 -
35 g10284.t5 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 23 34 -
33 g10284.t5 ProSitePatterns PS01187 Calcium-binding EGF-like domain signature. 47 73 -
34 g10284.t5 ProSitePatterns PS00010 Aspartic acid and asparagine hydroxylation site. 64 75 -
31 g10284.t5 ProSitePatterns PS00022 EGF-like domain signature 1. 73 84 -
30 g10284.t5 ProSitePatterns PS01186 EGF-like domain signature 2. 115 126 -
32 g10284.t5 ProSitePatterns PS00022 EGF-like domain signature 1. 115 126 -
38 g10284.t5 ProSiteProfiles PS50026 EGF-like domain profile. 8 45 22.305
36 g10284.t5 ProSiteProfiles PS50026 EGF-like domain profile. 47 85 12.772
37 g10284.t5 ProSiteProfiles PS50026 EGF-like domain profile. 86 127 16.58
26 g10284.t5 SMART SM00179 egfca_6 8 45 8.7E-10
29 g10284.t5 SMART SM00181 egf_5 11 45 4.5E-6
25 g10284.t5 SMART SM00179 egfca_6 47 85 2.6E-6
27 g10284.t5 SMART SM00181 egf_5 50 85 0.69
24 g10284.t5 SMART SM00179 egfca_6 87 127 0.15
28 g10284.t5 SMART SM00181 egf_5 89 127 3.8E-5
12 g10284.t5 SUPERFAMILY SSF57184 Growth factor receptor domain 4 127 5.02E-8
13 g10284.t5 SUPERFAMILY SSF57196 EGF/Laminin 8 52 7.65E-11
23 g10284.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 142 164 -

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:0005509 calcium ion 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