Sequence
atgc intronic sequence ATGC exonic sequence...gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 3
---gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
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cgtattcatttcagtcttttcttctt--gcatgtgaccttgttattcagtttaaatttgt-tttgatcctcatcctatccatgctcactctatttctgaccagGGTATTCGCCGACCTTGGAAAGGGGTTCTAATGTTTGGTCCACCTGGTACTGGAAAGACTCTTTTAGCGAAGGCAGTAGCTACAGAATGTGGCACAACAT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G054715_T01 (Zea mays), 3'ss of exon 3
gcttatc-tcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcag-gtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
| || | | | ||| || | | | ||| | | | || | | | | || || | | | || | | |||| ||| ||||| ||| | |||| |||||||| ||||||||||||||||| || || || || ||||| |||||||| || || || ||||| || ||||| |||||||
aatggtcatgaacccaactaatctattctctcttgtagcctttctcattta-gtctaaactctatacatagtggctaattatgtccactcttc-tttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCTACAGAATGTGGAACAACAT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G017305_T01 (Zea mays), 3'ss of exon 3
gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcag-gtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
| ||| | ||| | | | | || | || | | || || || | | | || | | | || |||| ||||| ||| | |||| |||||||| ||||||||||||||||| || || || || ||||| |||||||| || || || || || || ||||| |||||||
aatgatcatgaacccaaccaatcttttctctcttgtagcctttttcatctggtctaaacttgatacatagtggctaattatgtccacttttc-cttatcagGGTATTCGTCGACCTTGGAAAGGAGTTCTTATGTTTGGTCCACCAGGCACGGGAAAGACTCTTTTGGCAAAGGCAGTGGCCACCGAATGTGGAACAACAT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G03820.1 (Glycine max), 3'ss of exon 3
-gcttatctcactattattaaattaaga-atttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
| || || || | || | | |||| || || | || | | | |||| | || | ||| ||||| | ||| |||||||| |||||||| |||||||||||||| |||||||| ||||| || ||||| ||||||||| | |||||||| ||||||||||| ||||| || || |
ttttaataaagctcataacatatccacacattttgaatctcagtgaattaaatgtct-tggtgaatattgaagtttgagctcattatttctgttcttg-cagGGAATCAGGAGACCGTGGAAAGGTGTTCTCATGTTTGGACCTCCAGGAACTGGGAAGACACTTCTTGCTAAAGCAGTTGCTACTGAATGTGGGACCACTT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G22210.1 (Glycine max), 3'ss of exon 3
-gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
| || || ||| | || | | || || || || || | | | | | | | ||| ||||| | ||| |||||||| |||||||| ||||||||||| || |||||||| ||||| || ||||| ||||||||| | |||||||| ||||||||||| ||||| || || |
ttttaataaagctcgtatcatatacacacatttgaatctcagtgaattagatgtcttggtgaatattgaaatttggagctcattatttctgttcttg-cagGGAATCAGGAGACCGTGGAAAGGTGTCCTCATGTTTGGACCTCCAGGAACTGGGAAGACACTTCTTGCTAAAGCAGTTGCTACTGAATGTGGGACCACTT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G43840.1 (Glycine max), 3'ss of exon 3
gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT--------
|| | | | || | | | | ||| || | | || | | | || || | | || ||| | | || |||||||| |||||||| |||||||||||| | |||| || ||||| || ||||| ||||| ||| | ||||||| ||||||||||| |||||||| || |
--ttgtgaaattgttgtgacaacatgaagttca----ttcacacagtgaataatggagttcattgagaacattgtaattgtatgtgttaatgct--gcagggaataagGAGACCCTGGAAAGGTGTTATCGTGTTCGGACCTCCAGGAACTGGGAAGACGCTTCTTGCTAAAGGAGTTGCTACTGAATGTGGTACCACTTTCTTTAAC
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------gcttat-ctcactatta--ttaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttct-ttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
| || | | || | || |||| | |||| | ||| | || || || | | | | | ||| ||||||| | || | ||||| ||| | |||||||||||||| ||||| ||||||||||||||||| || || || || || ||||| ||||||||||| |||||||||||||| || |
gtactttgattctgctccatacgctgtgaaatttggattctatattactattattagacatggagcaatcatacagaataacagtttcaattcatcatttccgtagactttatatttgatcttc-caggtatagaggatacttaatttgattgtttttgtttcccttcagGGTATTCGAAGACCATGGAAAGGAGTTCTCATGTTTGGTCCTCCTGGGACAGGTAAAACCCTGTTGGCAAAAGCTGTTGCAACTGAGTGTGGTACCACCT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ06179 (Selaginella moellendorffii), 3'ss of exon 4
gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
| || ||| | | | | | ||| ||| | || ||| | ||||||||| | | ||||||||||||||||| |||||||| || || |||||||| || || || ||||| || || || |||||||| || || || || |
-----------------------------------------------gtgagcttgactatgtcactacctagaagacttaacgatttttt--ctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT
upper sequence: Vv09s0002g05260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ36428 (Selaginella moellendorffii), 3'ss of exon 4
gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggt-caagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
|| | | || | | | || | |||| || ||| | ||||||||| | | ||||||||||||||||| |||||||| || || |||||||| || || || ||||| || || || |||||||| || || || || |
----------------------------------------gtgagcttgactatgtcactacctagaagacttcaaggatttcgacgattttttctgtcagGGAATTCGTCGTCCATGGAAAGGTGTTCTGATGTTTGGGCCACCAGGTACTGGGAAAACTCTCTTGGCAAAGGCCGTGGCTACTGAATGCGGGACGACGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
ttttattgtttcttt CT-rich tract
ttttattgtttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttatctcactattattaaattaagaatttaagggacttttgtgttggaagtttgtattttttattcaggtcaagttttattgtttctttacttaacagGGAATTAGGAGACCATGGAAAGGTGTTCTTATGTTTGGTCCTCCTGGTACTGGCAAGACACTTTTGGCTAAAGCTGTTGCTACTGAGTGTGGTACAACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - ctcacta
- - - - - - - - - aaattaa
- - - - - - - - - - - - - - - - - - - - - gtgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggtca