Sequence
atgc intronic sequence ATGC exonic sequencegcaaagcatattcctctccttgttcctagctttctgcatctggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 6
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttatttta---aatccatactcatctgccttgttc--ttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
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---------------------------------gtatgttttacaccttttttcattcattgtgtgcttcactatcttttttaattttctaattca-ttgcagttttcaattctgttagGCCAATGGTGGCTTCATCATGAGTGCAAGCCATAATCCAGGTGGGCCAGATAATGATTGGGGTATCAAG
upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 6
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
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-----------------gtatgctttggatcttctataaattaa---ttatgt-ggatgactatccactttgtccattttttttttatttttgtatggtttctatattttttagGCCAATGGCGGCTTTATCATGAGTGCAAGCCATAATCCAGGTGGACCAGACAATGACTGGGGTATTAAG
upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 6
gcaaagcatattcctctccttgttcctagctttctg-catct-ggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
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gcatgccagttagagtttttctcctggagtattttgacatatagggataacataacctttcca-gctcacttgctcctttcttctg--atttcctcaaattttaa--------cagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 6
gcaaagcatattcctctccttgttcctagc-tttctgcatct-ggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
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gcatgccagttaaactttttctcctggagtattttggcatatagggatagcataacctttcca-gctcacttgcttttttcttctg------atttc---ccaaat--tttaacagGCAAATGGTGGATTTATTATGAGTGCAAGCCATAATCCTGGCGGACCTGAATATGATTGGGGTATTAAG
upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 6
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
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------------------------gcaagcttttta-atttatatcttcttacaaagttcaagatcgt--------ttttttcattactc--ttgttgataattattctcacagGCAAATGGAGGATTCATTATGAGTGCAAGCCATAATCCTGGTGGACCTGAATATGACTGGGGTATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
ttataac putative branch site (score: 2)
ttttataacacaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaagcatattcctctccttgttcctagctttctgcatctggcaccttattttaaatccatactcatctgccttgttcttttataacacaattaaaaccaaataatgtttcagGCCAATGGAGGTTTTATAATGAGTGCAAGCCATAATCCTGGTGGGCCTGAATATGATTGGGGCATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG