Sequence
atgc intronic sequence ATGC exonic sequence...acagactgaagaatagatttgatgttacacgtagaaatttgtgcatcttgctcaactttatgttttataacttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os09g15420.1 (Oryza sativa), 3'ss of exon 2
-----acagactgaagaatagatttgatgttaca---cgtagaaatttgtgcatcttgctcaacttta-tgttttataacttactt------------tgtcca----cct----tgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
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gtaaaacacgctataaaatagtattatctttttattcctttttacttcttttatacttttcaaaagcagcaatttgtaacatctctgtaaagtaaaagtatctaaattcctaaaatatgtcttttctagATTTGATGCTGTCGTTCATTTTGCTGGTCTGAAAGCTGTGGGTGAAAGTGTGCAGAAGCCATTGCTTTATTATGACCATAATGTTGCTGGGACAATAATT
upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G138410_T01 (Zea mays), 3'ss of exon 2
--------------------------acagac---tgaagaatagatttgatgttacacgtagaaatttgtgcatcttgctcaactttatgt-tttataacttactt-tgtccaccttgt-ttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
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gtaaagcttgctggaagattggcaatatatatctgttcataattaattaactattcaatgtttagccttgtcttctatgtaaatgcatctgcacctggtacttatttatatgcatgctacgctgttctccagATTTGATGCTGTTATTCATTTTGCTGGACTGAAAGCTGTTGGAGAAAGTGTACAAAAGCCTTTGCTTTATTATGACCATAATGTTGTTGGCACAATAAAT
upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G01940.3 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------acagactgaagaatagatttgatgttacacgtagaaatttgtgcatcttgctcaactttatgttttataacttactttgtccaccttgt-ttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
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gtaaggattttgacggaagcttctttctttattttttattttttattctaattagagtatgacggaagtttctttaatattattaaaaaaagatttatctgtcggtg----aatatgttctctttgtacatcattg-accttgcaactttttctcacctctttttcttttcttgcagATTTGATGCTGTCATACACTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT
upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G36850.1 (Glycine max), 3'ss of exon 2
------------------------------acagactgaagaatagatttgatgttacacgt-agaaatttgtgcat-cttgctcaactttat-gttttataact-tactttgtccacct-----tgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
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gtaaggatttggcagaaatttttataattgaaaaagaaaaaaatgattgttcttttctttgtcggtgcttcatgttttcttgtactagtttgttaagttgtaactgtttttcattcatgtatgtgtctttttcctgcagGTTTGATGCTGTGATACATTTTGCTGGGCTTAAGGCAGTGGGTGAAAGCGTGGATAAACCACTGCTCTACTTTGACAACAACTTGATAGGGACAATCGTT
upper sequence: Vv02s0025g01560.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G43540.2 (Glycine max), 3'ss of exon 2
----------------------------------------------------------acagactgaagaata--gatttgatgttacacgtaga--aatttgtgcatcttgctcaactttatgttttataacttactttgtccaccttgtt--tccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
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gtaaggattatgagagaagcttctttctttttatgattctgatttgagtatgacagaagttatttcaatattattaaaagagatttatatgtcggtgaatatgttctctttgtacatcatta-gccttgcaactttttctcacctcctttttcttttcttgcagATTCGATGCTGTCATACATTTTGCTGGACTGAAAGCAGTAGGAGAAAGTGTGCAAAAACCTTTACTATACTATAACAACAACTTGACTGGGACAATCACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgctcaactttatgttttataacttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
aacttac putative branch site (score: 2)
tccaccttgtttcc putative PPT
tttatgttttataact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acagactgaagaatagatttgatgttacacgtagaaatttgtgcatcttgctcaactttatgttttataacttactttgtccaccttgtttccactgcagTTTTGATGCTGTCATTCACTTTGCTGGGTTGAAGGCAGTTGGTGAAAGTGTGCAAAAACCCTTGCTTTACTTTGATAACAACCTTATTGGCACAATTACT
- - - - aagaata
- - - - - - - - - - - - - - - - agaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccacctt