Sequence
atgc intronic sequence ATGC exonic sequencegtgagttattactctataattatcatggaaatttctagattatcattctgtagcacctgaaacttaatcttttatatgatcaaagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os04g57350.1 (Oryza sativa), 3'ss of exon 11
gtgagttattactct-ataattatcatggaaatttctagattatcattctgtagcacct-----gaaactta--------atcttttatatgatcaaagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
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gtatattccttctcttgcactgattattctacttcatatttt-tcattatgttgcactcagaaagaagctaattgttagcatcttttacattgccaa-gCTACTGGATCATATAACCTTTGTGGACACTCCTGGAGTTTTATCAGGGGAAAAGCAGCGAACACAGCGTAGCTATGACTTCACTGGAGTTACATCATGGT
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G46350.2 (Glycine max), 3'ss of exon 11
gtgagttattactctataattatcatggaaatttctagattatcattctgtagcacctgaaacttaatcttttata--tgatcaaagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
|| |||| | ||| | | | || ||| | | || | | ||||| | || | | |||||| | || ||||||||||||| |||||||| ||||| || ||||| ||||||||||| |||||||||||||| ||||| ||||| || |||||||| ||||||||||| ||||
gtaagttgat---ctagatctgttcaaaaagtttacaagatttccctttatagcatttagaattgactctttttcaattgtccaaagCTACTGGAACACATCACATTTGTTGACACTCCGGGAGTTCTATCTGGAGAAAAGCAACGCACACAACGAGCATATGATTTTACGGGTGTAACATCTTGGT
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G10150.1 (Glycine max), 3'ss of exon 11
gtgagttattactctataattatcatggaaatttctagattatcattctgtagcacctgaaacttaatc--ttttatatgatcaa--------agCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
|| || | || || | | ||||| | || |||||| ||| || |||||| |||| ||| ||||| ||||| |||||||||| || ||||| || | ||||||||| |||| |||||||||||| ||||||| || || |||||||| ||||||||||| ||||
gtaagcttttctataccaaattaaaccaaaattaagatatatctcttctgtggcatttggaacttacctatttttttattatcaattatccaaagCTATTGGAGCACATTACATTTGTTGACAGCCCTGGAGTTTTATCTGGAGAAAAGCAAAGAACACATAGACAATATGATTTTACAGGTGTAACATCTTGGT
upper sequence: Vv19s0090g01130.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G20290.2 (Arabidopsis thaliana), 3'ss of exon 11
--gtgagttattactctataattatcatggaaatttctagattatcatt--ctgtagcacctgaaacttaatcttttatatgatca---------aagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
|| | | || || || | | | | | | |||| || ||||| | |||| || || ||| ||||| |||||||| | || ||||| || || ||||||||| ||||||| ||||| ||| ||||||||||||| || ||||| |||||||| ||||||||||
gtatgtttaacaacctcatgcttctgacaggagatcgttcattacttttgcctgtattgatttgctgataattgttgatccattcatctttgtttaagCTGCTGGAGCATGTAACATTTGTCGACACCCCTGGAGTTTTATCAGGGGAAAAACAAAGAACACAGCGAGCATATGATTTCACTGGTGTTACATCATGGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttctagattatcattctgtagcacctgaaacttaatcttttatatgatcaaagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
acttaat putative branch site (score: 4)
aaacttaatcttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttattactctataattatcatggaaatttctagattatcattctgtagcacctgaaacttaatcttttatatgatcaaagCTACTGGAGCACATCACGTTTGTGGATACTCCTGGAGTTCTATCAGGAGAAAAGCAACGAACACAGCGAGCCTACGATTTTACTGGTGTAACATCATGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA