Sequence
atgc intronic sequence ATGC exonic sequenceGGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattgaagcaattgctgattcattgctgatagttctactccattttgccttaacacaacctgtgttaacag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G459642_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g74310.4 (Oryza sativa), 5'ss of exon 14
GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattgaagcaattgctgattcattgctgatagttctactccattttgccttaacacaacctgtgttaacag
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GGGTCTTCTAGATGATACAGACTCAAGGGTAGCATATTATTCTGCTGCTTTTCTCTTGAAGgtatgcctatcacaattgttgattgtttgcttatagttctggtccactttga-ttgataaaaattatatgcacag
upper sequence: GRMZM2G459642_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA18G52540.1 (Glycine max), 5'ss of exon 14
GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatga--ttgaagcaattgctgattc---attgctgatagttctac-tccattttgccttaacacaacctgtgttaacag---
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GGAACTTTTGGATGACACAGATTCAAGAgtggcatattattcttctgcttttcttctgaaggcatggattttaattgacttttggtgttaaaaatgtgttagatccatatatatgaccttttgtaataacttctcattgctgcag
upper sequence: GRMZM2G459642_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G23240.1 (Glycine max), 5'ss of exon 18
GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatga--ttgaagcaattgctgat-----tcattgctgatagttctactccattttgccttaacacaacctgtgttaacag---
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GGAACTTTTGAATGACAGAGATTCAAGGgtggcatattattcttctgcttttcttctgaaggcatgaatttgatttcattttttgtgttgatcatgtgtattggtccataaatttcatcctttgtaacgatttccctttactgcagMapped 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|60346719|gb|DN213692.1|DN213692EST: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST:
gi|60399844|gb|DN232654.1|DN232654EST: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST:
gi|33091264|gb|CF051258.1|CF051258EST: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST:
gi|60344784|gb|DN211757.1|DN211757EST: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
EST:
gi|6056553|gb|AW090943.1|AW090943EST: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAG AGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTNAAAGCCTC
genomic: ATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTC
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:
48 (upstream exon),
48 (downstream exon)
Score:
127GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
Block sizes:
46 (upstream exon),
47 (downstream exon)
Score:
81GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
135GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
Block sizes:
48 (upstream exon),
47 (downstream exon)
Score:
75GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattga ... gtgttaacagAGAATGATGACAGAGGAACCAGAGATATACCAACGGATGCTTCAAAGCCTCATCTCAAAAGCTCAACAG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGGTCTTCTGGATGACACAGATTCAAGGGTAGCATACTATTCTGCCGCTTTTCTTTTGAAGgtatgattgaagcaattgctgattcattgctgatagttctactccattttgccttaacacaacctgtgttaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG