Sequence
atgc intronic sequence ATGC exonic sequence...aatgaacgttttctccacatttccctcactttcttttagtaacagcaatttgtttctatttcctttttctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os11g07490.1 (Oryza sativa), 3'ss of exon 2
aatgaacgttttctccacatttccctcactttcttttagtaacagcaatttgttt--ctatttcctttttctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
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--tgccaagtttcctagcagctgcaagtgttttttaatctggtaacacgtggtaagatagtttcgactactcataagctcttaaacatttggtgctttgcagATTGGTTATTGATAAAGAAACAGGGAAGCCAAAGGGTTATGGGTTTTGTGAGTACAAGGATGAGGAGACTGCTCTAAGTGCACGCCGGAACCTTCAAGGT
upper sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G096480_T03 (Zea mays), 3'ss of exon 2
aatgaacgttttctccacatttccctcactttcttttagtaacagcaatttgttt--ctatttcctttttctttatttatttatttatttattttgctt-cagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
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---ttctggtttggtaacactgattaacatgtttactactactgttaagtttttcagcatttgaatttgattttggtaactgactgctacaaattgcttgtagATTGGTGATTGACAAAGAGACCGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGATGAGGAAACTGCTTTAAGTGCACGCCGGAACCTTCAGGGT
upper sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G36350.1 (Glycine max), 3'ss of exon 2
aatgaacgttttctccacatttccctcactttcttttagtaacagcaatttgtttctatttccttttt--ctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
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--tgagattttttctgtaatttcttggaactgccttttgcttcttgaccaaaggtttatttggttgaagacttgaactattcccatcttcttttatccacagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACGGCTTTAAGTGCTCGACGAAATCTTCAGGGT
upper sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
aatgaacgttttctccacatttccct--cactttcttttagtaac-agcaatttgtttctatttcctttttctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
||| |||| || | || | | ||| ||||| | | | | |||| | | ||| | ||||| | || ||| || |||| | |||||||| ||||||| ||||| |||||||||||||||||||||||||| |||||||||||||| || || |||||||| || |||||||||||
--tgag-attttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttcttttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT
upper sequence: Vv18s0001g01800.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G71800.1 (Arabidopsis thaliana), 3'ss of exon 2
aatgaacgttttc--tccacatttccctcactttcttttagtaacagcaatttgtttctatttcctttttctttatttattta-----tttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
| | || || || | | | || | || | || ||| ||| | | | | ||| || || | |||||||| |||| ||| ||||||| || || |||||||| || ||||| ||||||||||| || ||||| |||||||||||||||||||||||||||||| |
-gtcagttttatcgttcaattatgatttagggttttgataaaggaaacacttttcttcaaacaaacgaaacacagaagcctaaaaaactttgctttattggattcagATTAGTTACGGATAGAGAAACTGGTAAACCAAAAGGCTACGGATTTTGTGAGTATAAAGACGAAGAAACAGCATTAAGTGCTCGTCGTAATCTTCAGAGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatttgtttctatttcctttttctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
tttcctttttctttat CT-rich tract
tttctatttccttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgaacgttttctccacatttccctcactttcttttagtaacagcaatttgtttctatttcctttttctttatttatttatttatttattttgcttcagATTGGTTATTGATCGAGAAACAGGGAAGCCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACAGCATTAAGTGCTCGTCGTAATCTTCAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
aatgaac
- - - - - - ctccaca
- - - - - - - - - - - ccctcac
- - - - - - - - - - - - - - - - - - -agtaaca