Sequence
atgc intronic sequence ATGC exonic sequencegtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g42540.1 (Oryza sativa), 3'ss of exon 3
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
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-------------------------gtatttcatgctctctgtttttttg-tatgaatctgtgtaggttcctcattaacttt---gttttatgtgtcgatgttttttcagCATTGGACAGTGATGATTTACTGTACCTAAAAGAACAAATGGAAGCTGAGGAAGACGCAGAGCGTCTTCTTCGCCGTACTGAGAAGCGTGCATTTGCTGC
upper sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G33570.2 (Glycine max), 3'ss of exon 3
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
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gtacagctctttttcccctgcttttgtgtgtctg-----tgttgcttgcacttcccgcctcacatgcttctttagtttacttcttcccttttaaaagtttaaatatgcagCCTTGGACAGTGATGATCTACTTTATCTCAAGGAGCAAATGGAAGCCGAGGAGGATGCAGAGCGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
upper sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA09G28980.2 (Glycine max), 3'ss of exon 3
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
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gtacagttctttttcccctgcttttgtgtgtctg---tgtgttgcttgcacttccgtttcacatgcttctttagtttctttcttcccttt--taaagtttaaatgtgcagCCTTGGACAGTGATGATCTACTTTATCTCAAAGAGCAAATGGAAGCCGAGGAGGATGCAGAACGCCTCCTGCGTCGCACTGAAAAACGGGCATTTGCTGC
upper sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ15111 (Selaginella moellendorffii), 3'ss of exon 3
gtactgtctctgcctctctctggctgggtttttggttccttt--ttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
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---------gtactgttcttcacttagtttttgaattccttgcatttctctaggaaaagctcgttttttttcttggttttctcacgttttcctgggaggttc---tttgcagCTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGG-----------------------------------
upper sequence: Vv16s0039g00280.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ16082 (Selaginella moellendorffii), 3'ss of exon 3
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
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---------gtactgttcttca-cttagtttttgaattccttgcatttctctaggaaaagctcgtttttttcttggttttctcacgttttc-ctgggagggtctttgcagCTCTTGACAGCGATGATCTTCTCTACCTCAAAGAACAGATGGAAGCCGAGGAGGATGCCGAGAGG----------------------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
ttagtttttttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgtctctgcctctctctggctgggtttttggttcctttttccttcaatatatacctttagtttttttttgtttttttttgaattttggttaagtttgaatatgcagCATTGGACAGTGATGATCTACTCTATCTCAAGGAGCAGATGGAGGCTGAGGAGGATGCAGAACGCCTTTTACGCCGCACAGAGAAGCGTGCCTTTGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC