Sequence
atgc intronic sequence ATGC exonic sequencegtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g42740.2 (Oryza sativa), 3'ss of exon 8
gtattgttcact-----tactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
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gtatagtccaatgtctatgcttgctgaaatatttatgtccatattactagtgtatgtacctctcatttgtt-ttctttgaacatttcagGTTATGTCTGGGTTCATGGGCTGAACATGGGGAGAGAACTGGTGGATTTTACGCTTGTAATCGCTATGAATCAGCAAAGAAGGAGGGAGTT
upper sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------gtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
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tgtatcttgtaatctgatcgtcatatgaatctggt-tgtgtaagattcttggttgctcacaatgaa-atctcattataaatagttgtgttgtttaaatgt-agGCTTTGCCTTGGGGCGTGGACAGAGCATGGTGAGAAGACAGGTGGCTTTTATGCTTGTAACCGTTATGAAGCAGCAAAGCAAGATGGCATT
upper sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 8
-----------------gtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
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gttatttttttttcaaattttaattcatatttagctttggagttctaaaaatgaacactttgtttcttcatgtatgctcttcgataatgtatgc-ttgcagGCTTTGTCTTGGTGCATGGTCAGATCATGGTGAGAGGACAGGTGGTTTTTATGCATGTAACCGTTATGAGACAGCAAAGCAAGAGGGAGTGMapped 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|87156257|gb|DY401046.1|DY401046EST: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
EST:
gi|26559055|gb|CA831290.1|CA831290EST: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
EST:
gi|31364271|gb|CD448626.1|CD448626EST: ATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: ATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
EST:
gi|213179909|gb|FM186344.1|FM186344EST: GGATGCATGCATATGACATGCACTCCTCCTTGTAAATTCGAATTTTGCTG GTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
EST:
gi|22549188|gb|BU101389.1|BU101389EST: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTG GTTATGTCTGGGTGCATGGTCAGATCATGGAGAGAGAACAGGTGGCTTTTA
genomic: GGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTA
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:
47 (upstream exon),
49 (downstream exon)
Score:
246CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
Block sizes:
46 (upstream exon),
47 (downstream exon)
Score:
261CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
Block sizes:
47 (upstream exon),
49 (downstream exon)
Score:
279CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
204CTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAATTTTGCTGgtattgttca ... cacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
ttctttgc CT-rich tract
atgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgttcacttactgcttgaaagaattgcagtattctgccatgtttatcttcttttgtcttgaggttctttgcacattccagGTTATGTCTGGGTGCATGGTCAGATCACGGAGAGAGAACAGGTGGCTTTTATGCTTGCAATCGTTATGAATCAGCAAAGAAAGAGGGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG