Sequence
atgc intronic sequence ATGC exonic sequence...aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattatgcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G40050.1 (Glycine max), 3'ss of exon 1
-aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattat-gcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
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agtagcttaaagcttgcg-tagcttattttcttgcttcctctccgtggtcctttgtaatagttggtatgaagtgctttta-tatgtcgatggtgttatgcagGTGGAGGCAATATTAGACAAGGAGAATTTCACTTTGGAAGAGCTTCTGGACGAAGAGGAAGTGATCCAAGAATGCAAGGCCTTAAACAGTCGTCTTATCA
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G29710.1 (Glycine max), 3'ss of exon 1
-aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattat-gcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
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agtagcttaaaacttgcg-tagcttattttcttgtttcctcttcaggctcctttgtaatagttgatttgaagtgctttta-tatgttgatggtgttttgcagGTGGAGACAATATTAGACAAGGAGAATTTCACTTTGGAAGAGCTTCTGGACGAAGAGGAAGTGATCCAAGAATGCAAGGCCTTAAACAGTCGTCTTATCA
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G08100.1 (Glycine max), 3'ss of exon 1
---------aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattatgcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
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tgtaattggagttcttgtagttgacgggggagaattttaagattgtgtcttgg--ttttatggtcaaactctcaagtg--gctgaaagtcttgtt-----tctctgcagGTGGAGGTAATATTGGACAAGGAGAACTTCACTTTAGAAGAACTTCTAGATGAAGAGGAAATAATCCAAGAATGCAAGGCCTTAAACAGTCGTCTTATCA
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G20500.1 (Glycine max), 3'ss of exon 1
aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattatgccc---ttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAG-CTTTGAATAGCCGCCTCATTA
||| | | || ||| | || | | | | || | ||||| | ||| | | | | || || ||||| |||||||| | |||| || ||||| || |||||||| ||||| ||||| |||||||| |||||||| ||||||||||| | | || || || || |||||
taattggagtccttataattgagtgggaag-aattttaaaattgtgtgttggttttatgttcaaactctctcaagaggctgaaagtcttgtt--tctctgcagGTGGAGGTAATATTGGACAAGGAGAACTTCACTTTAGAAGAACTTCTAGATGAAGAGGAAATAATTCAAGAATGCAAGGGCCTTAAACAGTCGTCTCATC-
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S188_88V6.1 (Physcomitrella patens), 3'ss of exon 1
aaatcttggatttcttacttgctt--tttttttggttctgacctaaccttttattattatgcccttctgttttattcttaatttttt-tcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
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---cgcggaagtgtggacttagttcgttgttttgaatttcatgcatattatttatgtaaagttttagttgctagtactgaagtggtcatggttgtacatgcagGTAGAAGCGGTGCTCGATAAGGATGCCTATACCTTGGAAGAACTCCTGGATGAAGATGAAATCATCCAGGAGTGCAAAGCTTTGAACAGCCGGCTTATCA
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S112_230V6.1 (Physcomitrella patens), 3'ss of exon 1
---aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattatgcccttctgttttattcttaatttttttcttattctctt-tagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
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ctgcacgctgcagttgaatatttg--tgtatattcgctttg--ctgataggtcattgatattttcttgctattagtgctaagtagtggctgtctacttatgcagGTTGAGTCGGTGCTCGACAAAGATGTCTACACCCTGGAAGAGCTCCTGGATGAGGATGAAATCATCCAGGAATGCAAAGCTCTTAATAGCCGCCTCATCA
upper sequence: Vv06s0004g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S391_39V6.1 (Physcomitrella patens), 3'ss of exon 1
-aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattatgcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
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atgcaataggggcacttggtttgttctttgtcgttgcgtgcatgtttttgcacagttgattgttgctgtta-atgaattgtggccgtggtcacgtatacagGTTGACTCGGTGCTGGATAAGGATGTCTACACTTTGGAAGAGCTCCTGGATGAAGATGAAATCATTCAAGAGTGCAAAGCTCTTAATAGCCG-------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttattattatgcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
tcttaat putative branch site (score: 3)
cccttctgttttattc CT-rich tract
tgttttattcttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaatcttggatttcttacttgctttttttttggttctgacctaaccttttattattatgcccttctgttttattcttaatttttttcttattctctttagGTGGAGTCAGTATTAGATAAGGAAAATTTCACTTTGGAAGAGCTTCTGGATGAAGAAGAAATAATCCAAGAATGCAAAGCTTTGAATAGCCGCCTCATTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - -tacttgc
- - - - - - - - - - - - - - - - - - - -cctaacc