Sequence
atgc intronic sequence ATGC exonic sequenceATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: 13113.m00246 (Oryza sativa), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtt-tctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag
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ATTGACCGTATCATAGCTAAAGGAGAGGAAACAACAGCTGAGCTTGATGCAAAAATGAAAAAGTTCACAGAGGATGCTATTAAATTTAAAATGGATGACAgtatgtacccttctcccgcagtctctttctttctatcactcaggtctaacttagtctttttatgcag-----------------------------
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA13G28720.1 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgt--tttctgtttctatttcttgtgact-tatt----ctctctttctgtgtcttctgtcaatctac-ctaacaccttttattttctgatgcag----------------
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ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCCGAGCTTGATGCCAAAATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtacctatgactacctgttctagctttaaaaacaatattggcatgctctttacaagttttatgctttcttctgtttgtagtttagagttactaatactgatactttcttttgtag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA17G02640.1 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag-----
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ATTGACAGAATTATTGCTAAAGGAGAGGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatgtaacctttgaatataatttctggctttgctaaagttggtttgattgatgatgttaaaaatctattttgttgtttaaatttctgtatatccacaag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G38050.2 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag-----
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ATTGACAGAATTATTGCTAAAGGAGAAGAAGCAACAGCTGAGCTTGATGCTAAGATGAAAAAATTTACTGAAGATGCTATCAAATTTAAGATGGATGACAgtatgtaacctttaaatataaattctggctttgctaaatttggtttgattgatgtcgttagaaatctattttgttgtttaaattcctgtatacccataag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA15G10370.1 (Glycine max), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgtt-ttctgtttctat--------ttcttgtgacttattctctctttctg-tgtcttctgtc---aatctac-----ctaacaccttttattttctgatgcag
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ATTGATAGAATTATTGCTAAAGGAGAGGAGGCAACTGCTGAGCTAGATGCCAAGATGAAGAAATTTACTGAAGATGCCATCAAATTTAAGATGGATGACAgtatgtgcctataattctagctttaaaaacaatattggcatgatctttacaagttttatgctttcttctgtctgtagtttatagttactaatactggtgctttctttttgtag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag
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ATTGATAGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAgtaagggtgtcacttac-ctactatttcc-----cctattaggt-tgtgtgaatattgtaatgttttga-taatctgttgttttatttgttgtag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag
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------AGAATCATTGCCAAAGGAGAAGAGGCAACAGCTGAACTTGATGCTAAGATGAAGAAATTCACAGAAGATGCTATACAGTTTAAAATGGATGACAGTAAGGgtgtcacttac-ctactatttcc-----cctattaggt-tgtgtgaatattgtaatgttttga-taatctgttgttttatttgttgtag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgt--acctgttttctgtttctatttcttgtgacttattc-tctctttctgtgtcttctg---tcaatctac---ctaacaccttttattttctgatgcag
|| ||| | || || ||||||||||| ||| ||||||| || |||||||| || ||||| || || || || ||||||||||||||||| |||||||||||||||| | | | || || | || | | ||| | ||| || || || || || || ||||| | | | | || | |||
ATAGACAGGATCATTGCTAAAGGAGAAGAGGCAACAGCTGAGCTTGATGCTAAGATGAAGAAATTTACAGAAGATGCCATCAAATTTAAAATGGATGATAgtatgtggatccactatccagggctctcactcattatttacttatctacttttgaaagttatggggctaaaatataatttaacatttatcctgctttgtt-cag
upper sequence: GRMZM2G010085_T01 (Zea mays), 5'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 5'ss of exon 14
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctat-ttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag
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ATTGATCGCATCATTGCAAAAGGAGAAGAAGCCACTGCTGAACTTGATGCCAAGATGAAGAAATTTACGGAGGACGCCATCAAATTTAAGATGGACGACAgtaagttctagt---gcgtttttgtgttctccttatctagcgtttcgtttaacag-----------------------------------------Mapped 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|87155727|gb|DY400516.1|DY400516EST: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST:
gi|32930781|gb|CF035593.1|CF035593EST: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST:
gi|31351381|gb|CD435738.1|CD435738EST: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST:
gi|6194488|gb|AW146592.1|AW146592EST: CAAATTTAAGATGGATGATA ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: CAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST:
gi|32930784|gb|CF035596.1|CF035596EST: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
EST:
gi|22546162|gb|BU098473.1|BU098473EST: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATA ATGCTGAATTGTATGACTTCGATGATGAGAAG
genomic: GAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
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),
32 (downstream exon)
Score:
356ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
Block sizes:
47 (upstream exon),
32 (downstream exon)
Score:
73ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
Block sizes:
49 (upstream exon),
32 (downstream exon)
Score:
72ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
Block sizes:
49 (upstream exon),
32 (downstream exon)
Score:
113ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacct ... tctgatgcagATGCTGAATTGTATGACTTCGATGATGAGAAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATTGACCGTATTATAGCTAAAGGAGAGGAGACAACAGCAGAACTTGATGCGAAAATGAAAAAGTTCACTGAGGATGCCATCAAATTTAAGATGGATGATAgtatgtacctgttttctgtttctatttcttgtgacttattctctctttctgtgtcttctgtcaatctacctaacaccttttattttctgatgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA