Sequence
atgc intronic sequence ATGC exonic sequencegtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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---------gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagt-tgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G342407_T01 (Zea mays), 3'ss of exon 4
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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---------------gtttgt----cacttacacattttatgaattt--gatggattttttccttacataaatccattaaatggtaattttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G355274_T01 (Zea mays), 3'ss of exon 3
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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---------------gtttgt----cacttacacattttatgaattt--gatggatttgttccttacataaatccattaaatggtaattttttgtagGACGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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-----gtctttatgccttctc--tggaatttttaattgta---attcatcgtagctgcattagcataaacgtttttt------ttcata----ctagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccactt-----------ttgtagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgag--tatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgc-tcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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-------------------gtag-actgttcgaagatttgctcagttggattggctcttttctcagcgg--------ctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC
upper sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
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----------------------gta-gactgttcgaa--gattttctcagttggattgctcttttctcagcgg----ctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
ttctgat putative branch site (score: 3)
tcttcat CT-rich tract
ttttatcttgttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG