Sequence
atgc intronic sequence ATGC exonic sequence...ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g51260.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------ctctttctctctctctctctaat-cacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtg-gcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
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gtaagtgctttattacgtttacatagttttttcagtcgcagatcaaagttcagagtttcagttcagagtttcttcagactagcttagtagttcagttcagtcagtttacttgggtttatgg-catcgatcggtgaacgtgttatccatgt--attgttgatggcatgcagGGTTGCAGAGATGTGGCAAGAGCTGCAGGCTGAGGTGGATCAACTACCTGAGGCCTGACCTGAAGAGGGGAAGCTTCTCGCAGCAGGAGGAGTCCCTCAT
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G42430.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------ctctttctctctctctctctaatcact---tttgcaggctaaccccacaatattt-tcatggctttct-----ctttgttttcttctggttaaat-cttgatggtg-gcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
|| || || | |||| | || ||| | | | || || ||| | ||| | | | ||||||| | || | | | ||||| |||||||| ||||||||||| |||||| | |||||||||||||| || |||||||| || ||||| || |||||| |||| ||||||||||| |||||
gtaattatatcactactctttctgtatatataaactctcatttaattttcttcattttcagtagttctcgatccaaaaaacttgtgaatttcctttttgtttttggccaaggcaacttatgaacttcttaattatatggttaattatttcacgaagtgcagGCCTGCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTTAGACCTGATTTGAAACGGGGAAGCTTCACTCCTCAAGAAGCTGCACTCAT
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G20440.1 (Glycine max), 3'ss of exon 1
----------------------------------------------------------------------------ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggc--agGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
| | | | | | | | ||| | | | | || || | | | ||| | || || | | | | | || ||||| || ||| || ||||| ||||||||||| |||||| | |||||||||||||| || |||||||| || |||||||| || |||||||| |||||||| || |||||
gtatatacacacacatatatagacatatataattaacaactctacactactattaatgtttttttcagcaccctctatatatgttattaatttctcagtttcttcattaagtaggtcttaaaactttctga-gtttttttattaattatatgttcataatttcatgatgtgtgcttagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTCAAGAAGCAGCCCTCAT
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G01050.1 (Glycine max), 3'ss of exon 1
-------------------------------------ctctttctctctctctctctaatcactt---ttgcaggctaaccccacaatat-tttcatggcttt----ctctttgttttcttctggttaaatcttgatg-gtggc-agGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
|| || | | | | || | | || | ||| || | | || | | | |||| |||| | | | || | | || ||||| ||| | ||| || ||||| ||||||||||| |||||| | |||||||||||||| || |||||||| || |||||||| || |||||||| ||||||| || |||||
gtatatatatacatatataattaacaagtctaccctactattaatatttttttcagcacccttttgtttctcagtttattcattaagtaggtcttaaaactttgagtttcttattaattatgtgttcatttcatgatgtgtgcctagGCCTTCAGAGGTGTGGAAAGAGTTGCAGATTAAGATGGATAAATTATCTAAGACCTGATTTGAAACGTGGAAGTTTCTCTCCTGAAGAAGCAGCCCTCAT
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G13890.2 (Arabidopsis thaliana), 3'ss of exon 1
-----------ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
| | | | | | | | | || | | |||| | | | || | | | || ||| || ||||| | | |||| ||||||||||||||||||| || ||| | |||||||||||||| || |||||||| | |||||||| ||||||||||| |||||||||||||| ||
gcacttatacacatatacatgggttttgtttcttgaattatctatactaat---aagaagtctttgtatttaggttttaatttctttgtggttttgcttgtgtttaattagGTTTGCAGAGATGTGGAAAGAGTTGTAGATTAAGATGGATAAATTATCTAAGACCTGATCTTAAACGTGGAAGCTTCTCTCCTCAAGAAGCTGCTCTTAT
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G13890.1 (Arabidopsis thaliana), 3'ss of exon 1
ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
| ||| ||| | | | | ||| | | | || | | | || ||| || ||||| | | |||| ||||||||||||||||||| || ||| | |||||||||||||| || |||||||| | |||||||| ||||||||||| |||||||||||||| ||
------------gtttcttgaattatctatac----taat---aagaagtctttgtatttaggttttaatttctttgtggttttgcttgtgtttaattagGTTTGCAGAGATGTGGAAAGAGTTGTAGATTAAGATGGATAAATTATCTAAGACCTGATCTTAAACGTGGAAGCTTCTCTCCTCAAGAAGCTGCTCTTAT
upper sequence: Vv09s0002g01670.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S149_164V6.1 (Physcomitrella patens), 3'ss of exon 1
-ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
| ||| | | ||||| ||| | | | | | |||| | | | | | ||| | | | | || ||||||| || | ||||||||||||||||||||| | ||||||||||| || |||| || || ||||| || || || | ||||| | | ||
cagaaagttttcttgattgccaatcagtttactatttttatac-attgaatttaaaaaaactaatgtctatttcgtcgatcacacacaattgctgtaacagGTCTTCAACGGTGTGGAAAGAGCTGCAGACTGCGGTGGATAAATTATCTCCGACCGGATTTGAAACGAGGAGTGTTTTCAGCGGCAGAAGAGAATTTGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
tcttgat putative branch site (score: 4)
ttaaatctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctttctctctctctctctaatcacttttgcaggctaaccccacaatattttcatggctttctctttgttttcttctggttaaatcttgatggtggcagGTCTGCAGAGATGTGGAAAGAGCTGCAGACTGAGATGGATAAATTACCTGAGACCTGACTTAAAACGTGGGAGCTTCTCTCCCCAAGAAGCTGCTCTCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -tctctct
- - - ctctctc
- - - - - - - - - - - - - - - gcaggct
- - - - - - - - - - - - - - - - - - - -ccccaca