Sequence
atgc intronic sequence ATGC exonic sequence...ggcaacttgaacggttcgacgctcagaagtagcaactacgctgaatatagacatgaacttgacactcaagtgatgctatttgggcgcttattgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 3'ss of exon 10
-ggcaacttg-aacggttcgacgctcagaagtagcaactacgctgaatatagacatgaacttgacactcaagtgat---gctatttgggcgcttattgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
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ctgcattctgcaaccattgaaagtgtagaat--gtcagtgtatagattataga-agaaattt--tacttaagtgagtagactaatttgtctttgtctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAG
upper sequence: GRMZM2G389362_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 3'ss of exon 10
-ggcaacttg-aacggttcgacgctcagaagtagcaactacgctgaatatagacatgaacttgacactcaagtgat---gctatttgggcgcttattgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
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cagcattctgcaaccattgaaagtgtagaat--gtcagtgtatagattataga-agaaattt--tacttaagtgagtagactaatttgtctttgtctgtatttagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCAGGCATTGCAGGATACGCAGTATACAAATACAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|32797899|gb|CD950135.1|CD950135EST: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAA GCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCT
genomic: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCT
EST:
gi|32920236|gb|CF025048.1|CF025048EST: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAA GCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCT
genomic: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCT
EST:
gi|67026759|gb|CO455508.1|CO455508EST: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAA GCAAAAGTGGAGCATCAGAAGCAGGCTGGGGCTTCTTGTGGGTCATCTTCT
genomic: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCT
EST:
gi|84908456|gb|DW404334.1|DW404334EST: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAA GCAAAAGTGGAGCATCAGAAGCAGGCTGGGGCTTCTTGTGGGTCATCTTCT
genomic: TGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCT
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
45 (downstream exon)
Score:
208TGTCAATGCAAAGAATGCAAATGCAAAAACACATGGGGAAGCTATGAGTGTGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
112TGTCAATGCAAAGAATGCAAATGCAAAAACACATGGGGAAGCTATGAGTGTGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
Block sizes:
48 (upstream exon),
46 (downstream exon)
Score:
70TGTCAATGCAAAGAATGCAAATGCAAAAACACATGGGGAAGCTATGAGTGTGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
Block sizes:
49 (upstream exon),
46 (downstream exon)
Score:
159TGTCAATGCAAAGAATGCAAATGCAAAAACACATGGGGAAGCTATGAGTGTGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaa ... ttgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatagacatgaacttgacactcaagtgatgctatttgggcgcttattgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
acttgac putative branch site (score: 159)
ttattgta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggcaacttgaacggttcgacgctcagaagtagcaactacgctgaatatagacatgaacttgacactcaagtgatgctatttgggcgcttattgtactcagGCAAAAGTGGAGCATCAGAAGCAGGTTGGGGCTTCTTGTGGGTCATCTTCTTTGGCCTTGTTGCAGCAGGAGTTGCAGGATATGCTGTGTACAAGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - -agtagca
- - - - - - - - - - - - - - - - - - - -gctgaat
- - - - - - - - - - - - - - - - - - - - - - - - - -catgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgct