Sequence
atgc intronic sequence ATGC exonic sequence...tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatatttgcctttttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g01870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G09390.1 (Glycine max), 3'ss of exon 10
-----tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatatttgcctttttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
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ggggagcgaataatttcttctgtatctactgtttttcatgcaccttaat---aataaagttatttgatatatataactgcatattcaaacttccc--tctgtcagGCACCATCGCGCAGTTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGTTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC
upper sequence: Vv04s0044g01870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G36030.1 (Glycine max), 3'ss of exon 10
tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatat--ttgcctt--tttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
|| | | | | | | ||| | || ||| | | | || || | ||| ||| |||| | || | ||| | | |||||||||||| || ||||||||||| ||||| |||||||||||||||||||||| |||||||||| ||||| |||||| || |||| ||||| ||||
----gtatctactgttttctttttcacctttgcaatttgttagtagtagtagataataaacttattttgatataactatatattcaaacattcgctttctgcagGCACAATCGCGCAATTGTTTGGAGCTGGTGAAGGTGAATGTTCTGTTATCATGCTATGGACATATGCTTTGGCCTCAGTTGCAGTCACTTTTTGGACAAC
upper sequence: Vv04s0044g01870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G32810.1 (Glycine max), 3'ss of exon 10
tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatatttgcct--ttttaatatgaaaatttgactcaactccc----taatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
|| ||| ||| || | |||| || | || | ||| || | || | | | | | || | || | | |||||||| ||| || ||||| ||| | ||||| ||||||||||||||||||||||| |||||||||| || ||||| || || | ||||||||||||||
-----tatttttacta-ttcagcgaagaacaaaaactatttttacatcagaaattcattaggcttaagtactcacaataaattttgttctcggtttattttggcagGCACTATTGCTCAATTGTTCGGATCTGGTGAAAGTGAATGTTCTGTTATCATGCTATGGACATATGCTTTAGCATCTATTGCAGTTACCCTTTGGTCAAC
upper sequence: Vv04s0044g01870.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G21930.1 (Glycine max), 3'ss of exon 9
tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatatttgcctttttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
| | || || | | || || | | || | | | || | || ||||| | || | | | |||| || ||||||| ||| || ||||| ||||| || || |||||||||||||| |||||||| ||||||||| ||||| |||| || | ||||||||||||||
gggaaccacttttcttttgtttcaactgttttcacattagaaattcgttagtcttggtattcataataaacccaattttgttctcactttaatttttcagGCACCATTGCTCAATTGTTCGGAGCTGGCGAAAGTGAATGTTCTGTGATCATGCTTTGGACATATATTTTGGCGGCAGTAGCAGTTACCCTTTGGTCAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggattatatttgcctttttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
ccctaat putative branch site (score: 3)
ctcccta CT-rich tract
atatttgcctttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgataatttcactggtttaagaaagagttgaagttcgttccttggattatatttgcctttttaatatgaaaatttgactcaactccctaatcttgcagGCACAATTATCCAGTTGTTTGGAGCGGGTGAGAGTGAATGTTCTGTTATCATGCTGTGGACATATGGCTTGGCATCAGTTTCACTCACCCTTTGGTCAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - -agaaaga
- - - - - - - - - - - - - - - - - - - -ttccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caactcc