Sequence
atgc intronic sequence ATGC exonic sequencegtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os08g32600.1 (Oryza sativa), 3'ss of exon 5
gtatctccttttttcttgcaaatggtattattatggaactccattac-ttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
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-------------gcatgaagagtattcgaattccgaattttgttgccttgaatgcttttgt-tgcgtgggttctaaatttgtaatgtgggattactgttttttcctat-attcagGGAGCAAATATACTTGTTGATAATAAAGGATGCATTAAGTTAGCAGACTTTGGGGCCTCCAAGCAAGTGGAGAAGTTG
upper sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g21510.1 (Oryza sativa), 3'ss of exon 5
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
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-----------gtactcaaaatctgaattctga--acacacaataatatgtatttattttaccacttgt-tgtgctcattatgattattcctgttatttgtcaaat----tccagGGAGCGAACATTCTTGTTGATAACAAAGGATGCATTAAACTTGCTGATTTTGGGGCATCTAAGCAAGTGGCAAAGTTG
upper sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G098828_T01 (Zea mays), 3'ss of exon 5
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
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---------gtatgcacgttga-agtcttaatatataatgcagatatttggccttgtttgttctgttgcaatgcttattctaat--gaacttgaaaattttgccaaat--ttcagGGTGCAAACATTCTTGTTGATAATAAAGGGTGCATCAAACTTGCTGATTTTGGGGCATCTAAGCAAGTTGCAAAGTTG
upper sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G39670.1 (Glycine max), 3'ss of exon 5
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
||||| | | | | |||||| | || | ||| | || || || | || | |||| ||| || |||| || || || || |||||||| || || ||||||||||| || |||||||||||||| |||||||||||||| |||
------------------------gtattgtgcttttattt--ttacttttttaagattttctgccttggtatttgtctctttatcatgttgatcaatgtgt-tgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCGCTGACTTTGGTGCATCCAAGAAAGTTGTTGAACTG
upper sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G28090.1 (Glycine max), 3'ss of exon 5
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
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---------------------------gtattgtgcat-----ttacttttataagattttctgccttggtgttcgtctctatatcatgttgatcaatg-ctttgctggatatagGGTGCCAACATTCTAGTTGATAACAAAGGGTGCATTAAACTCACAGACTTTGGGGCATCCAAGAAAGTTGTTGAACTG
upper sequence: Vv05s0020g02910.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G06030.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttct--acttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
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----------------------------------gtactttcctctttccaacatgtg-atatgcttgtggtttctcaaaattccgctataactctt----gtcatat-tctcctagGGGGCAAATATTTTGGTCGATAACAAAGGTTGCATCAGACTCGCAGATTTTGGTGCTTCCAAGAAAGTTGTAGAGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
ttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctccttttttcttgcaaatggtattattatggaactccattacttgtatatgtgcgcatgcttatgttttctacttgtgtctatatctcataatggccgtgcatcattcagGGGGCAAATATCCTGGTTGATAATAAGGGATGCATTAAACTTGCAGACTTTGGTGCATCTAAGAAAGTTGTTGAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA