Sequence
atgc intronic sequence ATGC exonic sequencegtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatttttttctgaaagcaagtttataactcatttacagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g10770.1 (Oryza sativa), 3'ss of exon 4
gtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatt-tttttctgaaagcaagtttataactcattta-cagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
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------------------------------------------gtacctttccccttgctaactgttgtactgtattgtatttagtactgtgatctttctgtatttatcgtcatatccccagatttgtgatattgtctcatggatcagGAATTTGAAGACACTCTAAAATACATTGAGAGTATACGGCCAATGGCGGAACCATATGGTATTTGCCGTATTGTCCCACCATCTTCTTGGAAGCCTCCAT
upper sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 4
gtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatttttttctgaaagcaagtttataactcattta----cagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
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--------------------------------------------------------gtttgttgcca-cattgtatagtatcagtacttttactgcactgaatttgt----ttttgcatacactaatcttatatctttctatggatcagGAATTTCAGGACACATTAAAATACATTGAGATTATCCGCCCAACAGCAGAACCATATGGAATATGCCGTATTGTTCCACCAGCTTCATGGAAGCCTCCAT
upper sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G140524_T02 (Zea mays), 3'ss of exon 4
gtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatttttttctgaaagcaagtttataactcattta-------cagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
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------------------------------------------------------------gtatcttatgttta-tcgcactgccttgtagtatggcagtacttggtttatttttgcatacactaatctcatgataccttcttgtggatcagGAATTCAAGGACACCTTAAAATACATTGAGAGTATACGGTCTACAGCAGAACCATATGGAATTTGTCGTATTGTCCCGCCGCCTTCATGGAAACCTCCAT
upper sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G31510.1 (Glycine max), 3'ss of exon 3
gtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatttttttctgaaagcaagtttataactcatttacagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT----------
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----------------------------------------------ttgaattcacttccgtccgtgtcactgttctgtttag-ttctgtcaattagctttatc-agaaaatctttctgacgccatttttttccc-------caggagtttcaagATACTTTGAAATATATATCAAGCATTCGCTCCAGGGCTGAGTCATATGGAATTTGTCGCATTGTTCCACCATCTTCTTGGAAACCCCCTTGTCCTCTCAA
upper sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 2
gtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatttttttctgaaagcaagtttataactcatttacagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
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------------------------------------------acatttgaattcacttctgtccatgtcactgttctgtttag-ttctgtcaattagctttatcagaaaatcatatctcttgacttgtcatt--ttttttcccagGAGTTTCAAGATACTTTGAAATATATATCAAGCATTCGCTCCAAGGCTGAGCCATATGGAATTTGTCGCATTGTTCCGCCATCTTCTTGGAAACCCCCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctattggcaaaatttataatttttttctgaaagcaagtttataactcatttacagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
ttataac putative branch site (score: 2)
ctcattt CT-rich tract
aaaatttataattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtattgtcacttggaatattcaaggcttccaatttaaaatattttcctctattcttgtttctttcattttctcatttgggttttttctattggcaaaatttataatttttttctgaaagcaagtttataactcatttacagGAGTTTGAAGACACTTTAAAATACATAGCAAGCATACGATCAAGAGCAGAACCATATGGAATTTGCCGAATTGTTCCTCCATCCTCTTGGAAGCCTCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG