Sequence
atgc intronic sequence ATGC exonic sequencegtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
gtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCA---------------GGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
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gtaatttcccttcccttttgctcctacaaatgttctttcaaattgttttacaaactagactagc-atacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT---------------
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G44600.1 (Glycine max), 3'ss of exon 3
gtaaattcatcc---tctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAG---------------GTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
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gtaatttcccccaccttttgctcctgccaaatactaatgtttcaaataccctgccaaatactaacatcatatccatggctgtgcaaattgtagGTTTTGATGGGGTTGAGATCCATGGGGCTCATGGCTACCTGCTTGAGCAATTTATGAAAGATAAAGTGAATGACCGAACAGACGAATATGGTGGATCCCT---------------
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
------------gtaaattcatcctctgataca---aatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttaca---caatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
| ||| | || | ||| | | | ||| || || ||| | ||| | || | | || | |||| | || ||||||||||||| ||||||||||| || ||||||||||| ||||||| || ||| | | | || || || | || | | | | |
gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatga--aatgtaatg-taagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
----gtaaattcatcctctgatacaaatcat---ggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttaca----caatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGA---------------CCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
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atgagtggagttgcactttaatgtatatgatataggcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaat-tgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT---------------
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA15G35410.1 (Glycine max), 3'ss of exon 4
------------gtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTC---AATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
|| | | || | ||| | | | | | || | | |||| | | | | | | |||| |||| ||||||||||||||||| |||||||| ||||| | |||| |||| ||| | || |||| | || | | ||| | || | |
tcatatacctgagtggagtttcactttaatatgatata-gtcatgatgttaaactgtgattctcaaagatattcaattcctaaccgcaattgcaat-tgtagGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTTTCTAATTGATCAGTTTTTGAAAGATCAAGTTAACGA-CAGAACAGACAAATATGGTGGATCCAC--
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ20558 (Selaginella moellendorffii), 3'ss of exon 4
gtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTC---AATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
| ||| ||| | |||||| | |||| ||| || | || || || |||| |||||||| |||||||||||||||||||| |||||||| | ||||| || || || | || | || ||| | || | |
---------------gtgttaaactatgctt---ctttctttctagtttc----atgggctaacgaaaa----------actgggtgtagGCTTTGATGGTGTTGAGATCCATGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAAATGGTGTCAACGA-TAGAACGGATGAGTATGGTGGTTCTTT--
upper sequence: Vv18s0041g02040.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EFJ28624 (Selaginella moellendorffii), 3'ss of exon 4
gtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTC---AATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
| ||| ||| | |||||| | |||| | || | || || || |||| |||||||| ||||||||||| |||||||| |||||||| | ||||| || || ||| | || | || ||| | || | |
---------------gtgttaaactatgctt---ctttctttctagtttc----acaggctaacgaaaa----------actgggtgtagGCTTTGATGGTGTTGAGATCCACGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAGATGGTGTCAACGA-TAGAACGGATGAGTACGGTGGTTCTCT-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
cactgat putative branch site (score: 3)
atgataatattgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaattcatcctctgatacaaatcatggcttagctttctagtcaatttcttcgatgcactgatgataatattgtttacacaatacatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTATCTACTTGACCAGGTCAATGATCGAACAGACAAGTATGGTAGATCACTAGAGAACCGTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA