Sequence
atgc intronic sequence ATGC exonic sequencegtaagatgctcattctgaatgtcaataccatgtcattattttattatttgcttgaccgtgttcttggtgtcacaagaatcactttttttcatccttccccatggcagggagtgatttttcattttattccttgtctttaaatagcttatgccaacttacctttattcaataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAGTTGAACGGGCTCAAACACTGCTTCTTAGCCTTGAGAGGGAGAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 5
gtaagatgctcattctgaatgtcaataccatgtcattattttattatttgcttgaccgtgttcttggtgtcacaagaatcactttttttcatccttccccatggcagggagtgatttttcattttattccttgtctttaaatagcttatgccaactta--cctttattcaataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAGTTGAACGGGCTCAAACACTGCTTCTTAGCCTTGAGAGGGAGAAG
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------------------------------------------------------------------------------------------gtctctttccaaccagtgtgatcatgatcatctttgtgacttatattttaaaggttatagtgaattgaagcatttcatttttttccccagAGGAGGATCGAGCTGCAAAGGAGGTTGAAGTCAGCCTTCTGATGGATGAAGTTGAAAGGGCTCAAGCACGATTAGTCAGTCTTGAGAGGGAAAAG
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 8
gtaagatgctcattctgaatgtcaataccatgtcattattttattatttgcttga--ccgtgttcttggtg-tcacaagaatcactttttttcatccttccccatggcagggagtgatttttcattttattccttgtctttaaatagcttatgccaacttacctttattcaataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAGTTGAACGGGCTCAAACACTGCTTCTTAGCCTTGAGAGGGAGAAG
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-----gtaatcaaa-tagttttcattttaatttta--gttgtacacttcacttgaatctgtaacatcagttcttacattactttataatctgcatattaagagttaaaagaccatgattctcc-taatattatttaatattgaagaaaatg----atcccctgttttcttgaaaacttcagAGGAAGAGAGGGCATCTAAGCAATCAGAGGTCAATCTTCTGATGGATGAAGTGGAACGTGCACAATCAATGCTTCTTAGTTTAGAAAGAGAGAAG
upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G09890.2 (Glycine max), 3'ss of exon 6
gtaagatgctcattctgaatgtcaataccatgtcattattttattatttgcttgaccgtgttcttggtgtcacaagaatcactttttttcatccttccccatggcagggagtgatttttcattttattccttgtctttaaatagcttatgccaacttacctttattcaataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAGTTGAACGGGCTCAAACACTGCTTCTTAGCCTTGAGAGGGAGAAG
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gtaaacaaatagttttcatt-tcaattttat-------tcttacacttaacttgaatctgtaacatcagttcttaca-ttattttataatatgcatattgagagttaagactgattctcc-taatattatttaatattgaagaaaatg----atcccctgttttcttgaaaacttcagAGGAAGAGAGGGCATCTAAGCAATCAGAAGTCAATCTTCTGATGGATGAAGTGGAGCGTGCACAATCAATGCTTCTTAGTTTAGAAAGAGAGAAGMapped 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|30301855|gb|CB978649.1|CB978649EST: ATTACATGAACTTGCACAAAGCCAGATGTTTGAACTTCGTGCCCAATCAG AGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAG
genomic: ACTACATGAACTTGCACAAAGCCAGATGTTTGAACTTCGTGCCCAATCAGgtaagatgct ... ataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAG
EST:
gi|30301790|gb|CB978584.1|CB978584EST: ATTACATGAACTTGCACAAAGCCAGATGTTTGAACTTCGTGCCCAATCAG AGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAG
genomic: ACTACATGAACTTGCACAAAGCCAGATGTTTGAACTTCGTGCCCAATCAGgtaagatgct ... ataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattccttgtctttaaatagcttatgccaacttacctttattcaataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAGTTGAACGGGCTCAAACACTGCTTCTTAGCCTTGAGAGGGAGAAG
caataac putative branch site (score: 2)
tttattcaataactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatgctcattctgaatgtcaataccatgtcattattttattatttgcttgaccgtgttcttggtgtcacaagaatcactttttttcatccttccccatggcagggagtgatttttcattttattccttgtctttaaatagcttatgccaacttacctttattcaataacttcagAGGAAGATACAGCAGCAAAACAATCAGAAGTCAGCCTTCTAATGGATGAAGTTGAACGGGCTCAAACACTGCTTCTTAGCCTTGAGAGGGAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA