Sequence
atgc intronic sequence ATGC exonic sequencegtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtggtatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0034g01790.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g49510.1 (Oryza sativa), 3'ss of exon 6
-----gtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtggtatgttaatatttt------cattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
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gtacattatcatatcatactgttgtgttgaatgttgttgtctatttgtacacatttgctatattaattctatgtatggtgttaatagGTCCGTTTTGTTGTCATGGGAAATATGTTTTGTACTGAACTGCGAATTCATCGTAAGTATGACTTAAAGGGCTCTACACAAGGCCGATCAACAAAGAAGC
upper sequence: Vv12s0034g01790.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G30320.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------------------------------------gtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtggtatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
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gtataacaaatatctgtctctagcttcttcttttcaattagtactactggtatgaataaccttgttttccaccccacctagtgagaaaagggttggttgttgttgtttttgtataaatatttctttctttcttcattggt----tgttgttttcatt---agGTTCGCTTTGTGGTCATGGGAAATATGTTCTGCACAGAACTTCATATTCACCGTCGTTATGATCTGAAGGGGTCTACTCAAGGAAGATATACAGACAAAG
upper sequence: Vv12s0034g01790.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G13450.2 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------------------------gtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtggtatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
| |||| | || |||| || |||| | | | | || || | | |||| | | | |||| || ||| |||||||||| ||||||||||| |||||| | | || ||||||||||||||| ||||||| || ||||||||||||||||| | |||
gtataacaaatacctgtctctagcttcttttaaattagtactacacatataaataaccttgttttccaccccacctggtgagaaaatggttggttgttgttgtttt--tattttcgtataaatatttctctttcttcat-tgattattgttttcattagGTACGATTTGTGGTCATGGGGAATATGTTTTGCACAGAACTTCATATCCACCGTCGTTATGATCTGAAGGGGTCTACTCAAGGAAGATATACAAAAGAAG
upper sequence: Vv12s0034g01790.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA08G19860.1 (Glycine max), 3'ss of exon 4
gtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtgg--tatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
||| || | | || || |||| | | ||| | || || || | | |||||| || ||||| || ||| | |||||||| ||| ||||||| || ||| ||| ||| ||||||||||||||| |||| || || || ||||||||||||||| | || |
gtatcacttgttatctctcttgagcttctttcatctcttttctttcaatttgaaataaatgattattttgtttaccagGTCCGTTTTGTCGTCATGGGGAATGTGTTTTGCACCGAACTACAAATCCACCGTCGTTATGATCTGAAAGGGTCTTCACAAGGAAGATATACAAACAACG
upper sequence: Vv12s0034g01790.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA15G05150.2 (Glycine max), 3'ss of exon 4
---------gtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtggtatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
|| ||||| ||| ||| || ||||||| | || | ||| | |||||| || |||||||| ||| |||||||||| ||| ||||||| |||||| ||| ||| ||||| || |||||| |||| || || ||||||||||||||| | || |
gtatcacctgttatgtttcttgagcttctttctct--tttctttcaaattgaaatgaatatatatttccttattttgtttaccagGTGCGTTTTGTGGTCATGGGGAATGTGTTTTGCACAGAACTACAAATCCACCGCCGATATGATCTGAAAGGGTCTAAACAAGGAAGATATACAAACAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctagtttctttttatttttgggaaggtggtatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
tgttaat putative branch site (score: 3)
ttttcattttc CT-rich tract
tatgttaatattttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggtttcccagtcttattttcctagtttctttttatttttgggaaggtggtatgttaatattttcattttcagGTGCGCTTTATGGTCATGGGAAATATGTTTTGTACAGAATTACGAATTCACCGTCGTTATGATTTGAAGGGTTCATCTCAAGGAAGATATACAGATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA