Sequence
atgc intronic sequence ATGC exonic sequence...tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaattttatgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g30020.2 (Oryza sativa), 3'ss of exon 4
tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaattttatgtaattatcatt----tgttttggtcattgatcggtg-tccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
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-----tgctttgggagattgtctggacggagttatttttcttcctgcaccaggcaatgatttccactgggatgctttaatgaatggtctgtaattgtctctgcagGAAGTATATGATCAACAAAAAGAACTTATTTTACTTGCGGAGCGAGTTGTACTTGCAACTCTTGGGTTTGATTTGAATGTGCATCATCCATACAAGCCTT
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 3
----tttttttcccagtgtggtttgatgtttgat-gcgattgaagatatatgaatttt-atgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
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ggacttcttttttgtatttacactcctcttttatagtggttctctttcctttacccttgatatatttat-atttgttt-----aatagaaattgtaaatgatgcagGAAGTGTACGAGCAGCAAAAAGAATTAATTTTACTTGGAGAGAGGGTTGTGCTTGCCACTTTAGGTTTTGATCTGAATGTTCAACATCCATATAAACCTC
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 3
----tttttttcccagtgtggtttgatgtttgat-gcgattgaagatatatgaatttt-atgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
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gactttttattttttatttacactcctcttttatagtggttctctttcctttacccttgatgtatttat-atttgtt-----caatagaaattgtaaatgatgcagGAAGTGTATGAGCAGCAAAAAGAATTAATTTTACTTGGAGAGAGGGTTGTGCTTGCCACTTTAGGTTTTGATCTGAATGTTCAACATCCGTATAAACCTC
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 4
-----tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaatttt-atgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
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ggacttcttttttgtatttacactcctcttttgtagtggttctctttcctttacccttgatatatttat-atttgtt-----caatagaaattgtaaatgatgcagGAAGTGTACGAGCAGCAAAAAGAATTAATTTTACTTGGTGAGAGGGTTGTGCTTGCCACTTTAGGTTTTGATCTGAATGTTCAACATCCATATAAACCTC
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G45190.2 (Arabidopsis thaliana), 3'ss of exon 6
tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaattttatgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
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actttgcttcgttgttttgtagaaccatggtcctttggtcctgatttattgtctgttggtcagcatatcaaaatgtatttgacctatatcactttttcagGAAGTATATGAGCAACAAAAAGAGCTTATATTAAACGGAGAAAAAATTGTTCTTTCCACTCTAGGCTTTGACCTCAATGTTTATCATCCTTATAAACCCC
upper sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 5
tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaattttat-gtaattatcatttgttttggt--cattgatcggtgtccacaat-gcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
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----cctcctatgatcattgtccttgtcgttggatctctcatctgtgctggtcaccgtctctattatttctcttctttgtactgaacgtatttcacttttgcagGAAGTATATGAGCAACAAAAAGAGCTTATACTAAATGGAGAAAAGATTGTACTTTCTACGCTGGGATTTGACTTCAATGTTTATCATCCTTATAAGCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgaattttatgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
cattgat putative branch site (score: 4)
tttatgtaattatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttttttcccagtgtggtttgatgtttgatgcgattgaagatatatgaattttatgtaattatcatttgttttggtcattgatcggtgtccacaatgcagGAAGTATATGAGCAACAAAAAGAGCTAATTTTAATTGGAGAGAGGGTTGTACTTGCAACTCTAGGTTTTGACCTCAATGTTCACCACCCATATAAACCCC
- - tttccca
- - - - - - - tggtttg
- - - - - - - - - - - - -ttgatgc