Sequence
atgc intronic sequence ATGC exonic sequence...tgaagttgcactacttgttcctttttttaaaacgaaacttgagatgtgggtgtgtatgtgcatctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g15020.1 (Oryza sativa), 3'ss of exon 3
--tgaagttgcactacttgttcctttttttaaaacgaaacttgagatgtgggtgtgtatgtgcatctcttgagctgataaatggtt-ttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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gccttttttaatcaacctactgtgcttcatactatcatgttcttagcttcctattgc-cataaaactgtcaaattatcaactatctgttgttttcttg--cagGGAAAATGAACAGCTGTCTAAGTACGGGGATACCAAATCTGCTCGCAGTATAATGCTGATTGAGCTCAAAAAACTTATTGAAGCGAACCCCCTTTTCCGG
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 3
--tgaagttgcactactt-gttcctttttttaaaa---cgaaacttga-gatgtgggtgtgtatgtgcatctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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tactatcctacagtgttttattccaagtattataattccttagcctgctgcttctgttttcaatttgtagctca-aaactatcaaataatgttgcttg------cagGGAAAATGAACAGTTGTCTAAGTATGGGGATACTAAATCAGCTCGAAGTATTATGCTGGTTGAGCTAAAAAAACTTATTGAAGCAAACCCCCTTTTCCGG
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------tgaagttgcactacttgttcctttttttaaa----acgaaacttgagatg-tgggtgtgtatgtgcatctcttgagctgataaatgg------ttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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gtaatatcttgaatatgtaatttaacggaatgcattgcttttcagtgtcttctcttgactgttaggtggatgagattgtatgtctaattcatatctcaattcttcatgaattttgattcactactcagattaattaaagtggtaacttgacaattgagtgttattttgtttcacataacagGGAGAATGAGCAGCTGTCCAAGTATGGTGACACCAAAACTGCTCGAAGCATTATGCTGATAGAACTGAAAAAACTCATAGAGGCAAATCCTCTTTTCCGT
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------tgaagttgcactacttgttc----ctttttttaaaacgaaacttgagatgtgggtgtgtatgtgcatctcttgagct-gataaatgg------ttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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gtaataccttgaatgcattgcttgtcagtgtctttgactgttaggtggatgagatcgtgcatctaattcatatctcaattcttcatgaattttgattcacaactcagattagttaagtggtaagcttgacaattgagtggtattttgtttcacataacagGGAGAATGAGCAGCTATCCAAGTATGGTGACACCAAAACTGCTCGAAGCATTATGTTGATAGAACTGAAAAAACTCATAGAGGCAAATCCTCTTTTCCGT
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 4
tgaagttgcactacttgttcctttttttaaaacgaaact-tgagatgtgggtgtgtatgtgca--tctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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gagaaggatggagattgtgaagaaccaagttaccatactgtgtcatgttgactttttattgcaagactgtttagttttt---cctttccatttcaaatgccagGGAGAATGAACAGCTGTCTAAGTATGGCGACACCAAAACTGCTCGAGGGATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G41840.1 (Glycine max), 3'ss of exon 3
-tgaagttgcactacttgttcctttttttaaaacgaaacttgagatgtgggtgtgta--tgtgcatctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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gagaggatggagattgtgaagaactaagtttactatattgtgtcatgttgactttttattgtaagactgtttagttttt---cctttcaatttcaaatgccagGGAGAATGAGCAGCTGTCCAAGTACGGTGACACCAAAAATGCTAGAGGAATTATGTTGATAGAGCTAAAAAAGCTCATAGAGGCAAATCCTCTTTTCCGT
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 3
--tgaagttgcactacttgttcctttttttaaaacgaaacttgagatgtgggtgtgtatgtgcatctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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tgtttggatgtgaaagagggtgtgatactcgagtttctctctcgattgtttgcgttt-tgtggattgaaatttgacatcaatgatttt-catgaatctgcagGGAAAATGAGCAGCTTTCAAAATATGGAGACACTAAAACTGCTCGGGGCATAATGCTAGGCGAACTTAAAAAACTAATTGAAGCGAATCCACTTTTTCGT
upper sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------tgaagttgc-actacttgttcctttttttaaaacgaaacttgagatgtgggtgtgta----tgtgcatctcttga-gctgataaatggtttt---------gctttaaa--------aatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
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gttagggtcttcgccagcacaatgacagttttaatggagaccacattttactgtcagcaagtgcatttcctgttatatgtagcttccattgaaggggttttgtagaggtgctcagatagcctcatggaactatgagtgcttgtaactaagtttatcatcactgctgtggattcgtttggttcagGGAAAATGAGCAGCTGTCAAAGTACGGAGACACCAAATCTGCTAGAAACATTATGCTTCTAGAACTCAAAAAACTAATAGAAGCCAATCCACTCTTTCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgggtgtgtatgtgcatctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
agctgat putative branch site (score: 4)
ttttgcttt putative PPT
ttttgctttaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaagttgcactacttgttcctttttttaaaacgaaacttgagatgtgggtgtgtatgtgcatctcttgagctgataaatggttttgctttaaaaatcagGGAAAATGAGCAGCTGTCCAAGTATGGTGACACCAAGACAGCTCGTAGCATAATGCTGATAGAGCTTAAAAAACTAATTGAAGCAAATCCTCTTTTCCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - ctacttg
- - - - - - - - - - - - - - -aaacgaa
- - - - - - - - - - - - - - - - - - - - - - - -gggtgtg