Sequence
atgc intronic sequence ATGC exonic sequence...ctttttaatttattattgctgttgtaccttgttggtaatgtttgttaagtttgtcattctaatcctagttggtttcttttttctgggttatattctatagCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0014g01170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g13370.1 (Oryza sativa), 3'ss of exon 10
ctttttaatttatt-attgctgttgtaccttgttggtaatgtttgttaagtttgtcattctaatcctagttggtttcttttttctgggttatattctat-agCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
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-tcatggatgggtttaaccctcttacaacttctta-taccttgtattcttgttcaattttaagtagctgtaatatgttttgcactaatatatttcctatcagCAAAGCTACAGGGTTAGATGGGACATTTCCTCCTGCTTGGATTGGTACTGGTATTGCTTATGCTGCACAGGAGGAGGGTGATCAAGCAATGGCTGCATTT
upper sequence: Vv19s0014g01170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G166684_T02 (Zea mays), 3'ss of exon 9
ctttttaatttattattgctgttgtaccttgttggtaatgtttgttaagtttgtcattctaatcctagttggtttcttttttctgggttatattctat-agCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
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-acttttatgtttcactggaacgtggaatgattctaaatttctaattgataaaacttggtaggtactgtggttttctatacattaatctgttttctttcagCAAAGCTACAGGTTTAGATGGGGCATTTCCTCCTGCTTGGATTGGTACAGGCATTGCCTATGCTGCTCAAGAGGAGGGTGACCAAGCAATGGCTGCGTTT
upper sequence: Vv19s0014g01170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G147603_T01 (Zea mays), 3'ss of exon 10
ctttttaatttattattgctgttgtaccttgttggtaatg--tttgttaagtttgtcattctaatcctagttggtttcttttttctgggttatattctat-agCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
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--cattgatccatgcaaacttttatgtttcactgg-aatgattttaattgataaaacttggtaggtactgtggtttacagtacattaatatgttttctttcagCAAAGCTACAGGTTTAGATGGGACGTTTCCTCCTGCTTGGATTGGTACAGGCATTGCCTATGCTGCTCAAGAGGAAGGTGACCAAGCAATGGCTGCATTT
upper sequence: Vv19s0014g01170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G32850.1 (Glycine max), 3'ss of exon 9
-ctttttaatttattattgctgttgtaccttgttggtaatgtttgttaagtttgt-cattctaatcctagttggtttcttttttctgggttatattctatagCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
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tctgcatgaataattatcaagg--gttcattatttatgcctttgattgtttttgaacatcattatcgaaacttattgttcaatttcattgtgtactgtacagCAAGGCAACTAGTCTAGATGGAACATTTCCCCCTGCATGGATAGGCTATGGGAATGCTTATGCTGCTCAAGAAGAGGGAGACCAGGCTATGTCTGCTTAC
upper sequence: Vv19s0014g01170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G25700.1 (Glycine max), 3'ss of exon 9
ctttttaatttattattgctgt-tgtaccttgttggtaatgtttgttaagtttgt-cattctaatcctagttggtttcttttttctgggttatattctatagCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
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-gtttgaatttga-attatcatgcgttcattatttacgcccttgattgtttttgaacatcattatcaaaacttattgatcaatttcattgtgtactgtacagCAAGGCAACTAGTCTAGATGGAACATTCCTCCCTGCATGGATAGGCTATGGGAATGCTTATGCTGCTCAAGAAGAGGGTGATCAGGCTATGTCTGCTTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taagtttgtcattctaatcctagttggtttcttttttctgggttatattctatagCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
ttctaat putative branch site (score: 2)
ttatattctata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttttaatttattattgctgttgtaccttgttggtaatgtttgttaagtttgtcattctaatcctagttggtttcttttttctgggttatattctatagCAAGGCTGCAAATCTAGATGGAACATTTCCTCCTGCTTTGATAGGTTGCGGAAATGCTTATGCTGCTCAAGAAGAGGGTGACCAAGCAATGTTGGCCTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - tgctgtt
- - - - - - - - - - - - taccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - gtcattc