Sequence
atgc intronic sequence ATGC exonic sequencegtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os04g47240.2 (Oryza sativa), 3'ss of exon 6
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgt-tcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
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-------------------------gtagcaatttc---tttggttttctctcttt--tctttggtttgtttgtatcggtggaattatggtgtaattataagtcctgttcatcacaattt---tgcagGGATATTAAAGGTGCAAATATACTAGTAGATCCTAGTGGTCGTGTTAAGCTTGCAGATTTTGGAATGGCAAAACAT
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G37730.1 (Glycine max), 3'ss of exon 7
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
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-------------------gtaaactaagtcatct-attcatgatttcaatgt-ttaaaactttaatttattgctaagttctga--tgtagtgatgtctatctctgaaataccttttatttgtgaagGGATATCAAAGGAGCAAATATACTGGTAGATCCAACTGGTCGGGTCAAGTTGGCAGACTTTGGCATGGCAAAACAT
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G30100.1 (Glycine max), 3'ss of exon 6
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgttcaccttttttctcacaaaccatattt-cctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
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-------------------gtaaactaaatcatct-attcatgatttcaatgtttaaaactttaagttgttg--ctaagttctgatgcagt--gatgtctatatctgaaattgcatttatttgtgaagGGATATCAAAGGAGCAAATATACTGGTAGATCCAACTGGTCGGGTCAAGTTGGCAGACTTTGGCATGGCAAAACAT
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G24970.2 (Glycine max), 3'ss of exon 5
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttca-aactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
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gtaaacagagtcacttgttcat--ttttaaaaccttaaattttactgctgcctcataatgatta----attttttatactccagagtcctgatatatatctatcacttacattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT
upper sequence: Vv16s0050g00770.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G30030.2 (Glycine max), 3'ss of exon 6
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
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gtagacagagtcacttgttcatt-tttaaaactttgaatttta-ctgcttcctcataatg-----attaatttttatacttcagagtcctgatatatatctatcacttaattgcatttcttgtaaagGGACATCAAAGGAGCAAATATACTGGTAGATACTAATGGCCGGGTTAAGTTGGCAGACTTTGGCATGGCAAAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctttatttcaaactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
ttctcac putative branch site (score: 2)
tatttcct putative PPT
atttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatcaagttaccaattgttgatccaacaatctgaagtgtagctgctttttattgatttttctattatttgctttatttcaaactttgttcaccttttttctcacaaaccatatttcctgtacagGGATATTAAAGGGGCAAATATACTTGTAGACCCAAGTGGTCGAGTCAAGTTAGCAGATTTTGGAATGGCAAAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG