Sequence
atgc intronic sequence ATGC exonic sequence...ttcaaaggagaacaaatattcatacctactttatgtggctaccttgcttcagttaccgatggttattgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g01500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g41740.1 (Oryza sativa), 3'ss of exon 2
ttcaaaggagaacaaatattcatacctactttatgtggctaccttgcttcagttaccgatggttattgacatgttgtattcaac------tcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
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---ctcctagtacacctatgctgacctgat--atttgagcactcataagcgtttaactaatatatttgtccagccatacataaccatgcgtttctcttt-ctgcagAAAAGGAAAACTTGTGCCTTTATGGGTTTCCCAATGAGCATTGGGAAGTAAATTTGCCCGCAGAAGAGGTGCCACCTGAGCTCCCAGAGCCAGCATTGGG
upper sequence: Vv11s0016g01500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G038066_T02 (Zea mays), 3'ss of exon 3
----------ttcaaaggagaacaaatattcatacctactttatgtggctaccttgcttcagttaccgatggttattgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
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atcccctgttttcataatgagatgtatactgat-cgtgttattaataattaccacagatatatttctacagctta---gcatgac-----caagt-gttctcttttgcagAAAAAGAAAACTTGTGCCTGTATGGGTTTCCTAATGAGAGCTGGGAAGTAAATTTGCCTGCTGAAGAGGTGCCACCTGACCTCCCAGAACCAGCATTAGG
upper sequence: Vv11s0016g01500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G014780_T01 (Zea mays), 3'ss of exon 1
--ttcaaaggagaacaaatattcatacctactttatgtggctaccttgcttcagttaccgatggttattgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
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catctcatttatcgtaataaggtgtctactgaccatgttattaataattaccacatatatatttct-ctgacttagcatgaccaagt-gttctcttttgcagAAGTAGAAAACTTGTGCCGGTATGAGCTTCCAAATGAGAGCTGGGAAGTAAATTTGCCTGCTGAAAAGGTGTCTCCTGAGCTCCCAGAACCAACATTAGG
upper sequence: Vv11s0016g01500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G05940.2 (Glycine max), 3'ss of exon 2
-ttca--aaggagaacaaatattcatacctactttatgtggctaccttgcttcagttaccgatggtt-attgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
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gttaattgatgagagtagagcacgttaacaatgcaagtgaggtacactgata-atatactgatgcttcatttgtttaac-tgttgtgtttattttgcac--cagAAAAGGATAATCTTTGTCTGTACGGATTCCCTAATGAGCAATGGGAAGTTAATTTACCTGCGGAAGAAGTTCCTCCGGAGCTTCCTGAGCCTGCATTGGG
upper sequence: Vv11s0016g01500.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G16740.1 (Glycine max), 3'ss of exon 2
-----ttcaaaggagaacaaatattcatacctactttatgtggctaccttgcttcagt-taccgatg-gttattgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
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ttcgtgtttgctatgctcaaattcttttaacaatccaagtgagctgcattgtgataatatgctgatgcattccttaactgttgtgttta-------ttgtgcaccagAAAAGGATAACCTTTGTTTATACGGGTTCCCTAATGAGCAATGGGAAGTTAATTTACCTGCGGAAGAAGTTCCTCCGGAGCTTCCTGAGCCTGCATTGGGMapped 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|71876744|gb|DT025799.1|DT025799EST: ATGTTGAAGAGTTCTACCAGCAATGCGATCCCG AGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTA
genomic: ATGTTGAAGAGTTCTACCAGCAATGCGATCCCGgttagggttt ... tatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTA
EST:
gi|110702780|gb|EE079049.1|EE079049EST: ATGTTGAAGAGTTCTACCAGCAATGCGATCCCG AGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTA
genomic: ATGTTGAAGAGTTCTACCAGCAATGCGATCCCGgttagggttt ... tatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcagttaccgatggttattgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
aactcac putative branch site (score: 2)
ctcactct CT-rich tract
tctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaaaggagaacaaatattcatacctactttatgtggctaccttgcttcagttaccgatggttattgacatgttgtattcaactcactctatattgcagAGAAGGAAAATCTTTGCCTTTATGGATTCCCTAATGAACTGTGGGAAGTTAATTTACCTGCTGAAGAGGTGCCGCCTGAGCTCCCTGAACCTGCCTTAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- caaagga
- - - - -gaacaaa
- - - - - - - - - - catacct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactc