Sequence
atgc intronic sequence ATGC exonic sequence...tggtttttcttgtggtccttttttaaatgatctcaaaatttcatccataaagaagatgatgacaatatttcttttgatttaattatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 8
tggtttttcttgtggtccttttttaaatgatctcaaaattt-catccataaagaagatgatgacaatatttcttttgatttaat--tatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
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--atgtaagttgtgatgaaatagtaaatt-tctcaattcgaacttacatgcaaaatatgcttgatacttctcaattacctaagtgctttattgttgcattcagGAACATCTGTCAAAAGATGATGCAAGGCAACAGTTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCAGTTTTCTTCAGTGTCCGGAAGATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 9
----------------tggtttttcttgtggtccttttttaaatgatctcaaaattt-catccata--aagaagatgatgacaatatttcttttgatttaattatgttgctgtatat-agGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
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gtatttatctagctcttgaactttatatttattagtctatcaatatatttacaatttgcgtccacattggtaaagcctcattagaactctagcttatctgagtactccgtttgatttcagGAACATTTATCAAAAGACGATGCACGGCAACAATTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCTGTTTTCTTTAGTGTCCGTAAGATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 8
----------------tggtttttcttgtggtccttttttaaatgatctcaaaattt-catccata--aagaagatgatgacaatatttcttttgatttaattatgttgctgtatat-agGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
|| | | | | | | | | || | | ||||| | | || | || | | | | | | | | || || | || ||||||| || |||| || |||||| | ||||||||||| || ||||| || || || || |||||||| || |||||||| |||||||| ||||||||||
gtatttatctatctcttgaactctatatttattagtctgtcgatatatttacaatttgcgttcacattggtaaagcctcgttagaactctagcttacctgagtactctgtttgattccagGAACACTTATCAAAGGACGATGCACGGCAACAATTTCTCAGAATCTTAAGGACTCTTCCATATGGGAACTCTGTTTTCTTCAGTGTTCGGAAGATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 13
tggtttttcttgtggtccttttt-taaatgatct-caaaatttcatccataaagaagatgatgacaatatttcttttgatttaattatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
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--gcttctagcctatactttatagtaaatgaaatatactgctgggtttctttgtattttttttcctccccttccataatattttttttatctctttaattagGAGAATCTGACAAAAGATGATGCGCGACAACAATTTCTGCGTATATTGAGAGCACTTCCTTATGGAAATTCTGTTTTCTTCAATGTTCGCAAGATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 10
tggtttttcttgtggtccttttttaaatgatctcaaaatttcatccataaagaagatgatgacaatatttcttttgatttaattatgttgctgtatat------agGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
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tattttcttctagcatatactttatagtaaatgaaatatactgct------gagtttctttatattttttcctccacttacataatgtttttttctcttttattagGAGAATCTGACAAAAGATGATGCGCGGCAACAATTTCTGCGTATATTGAGAGCACTTCCTTATGGAAATTCTGTTTTCTTCAATGTTCGCAAGATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 10
tggtttttcttgtggtccttttttaaatgatctcaaaatttcatccataaagaag-atgatgacaatatttctt--ttgatttaattatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
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-tttaatcatggaaatcaatatctgcttcaagtatacctattacatatgatgaaatatgccgattttctgccttgtctgatttaag-atgtt-ctcttcacagGCGCATGTGACGAAAGATGATGCTAGACAACAATTTCTTCATATATTGAGAACACTTCCCTATGGGTTTTCCGTTTTCTTCAATGTTCGCAAAATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 10
tggtttttcttgtggtccttttttaaatgatctcaaaatttcatccataaagaag-atgatgacaatatttct--tttgatttaattatgt-tgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
| | | || | ||| | | | | | | | || | ||| ||| ||| | | || | |||||||| | || | | | | ||| ||| |||||||||| ||||| ||||| |||||||| || ||||||||||| || |||||| ||| |||||||| | ||||||||| |||||||
----aatcatggaaatcaatatttgcttcaagtatacctattacatatgatgaaatatgctgattttctgccttatctgatttaagaaggtgttcctttcacagGCGCATGTGACAAAAGAGGATGCTAGACAGCAATTTCTGCATATATTGAGAACACTTCCCTATGGGTTTTCTGTTTTCTTCAATGTTCGCAAAATTGATG
upper sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------tg-gtttttcttgtggtccttttttaaatgatct----caaaatttcatccataaagaagatg--atgacaatatttcttttgatttaattatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
|| |||| |||| ||| ||| | | || |||| | |||| | |||| ||| || || ||| | | ||||| | | || ||||| | |||| ||||||||||||||||||||||||||| |||| ||| ||||||| || |||||||| ||||| ||||| || |||||||| ||||
gtaggaatagttctatgcattttgattgtcttcccctttctagatacctttggcaaataaaaacccattgaagtgatggcatggtaaaatgatatttcgtatgtgtatgtgg--gcatgtagGAGAACGTGACCAAAGATGATGCAAGACAACAATTTCTACGGATACTGAAGGCACTGCCATACGGGAATTCAGTTTTTTTTAGCGTACGCAAGATAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataaagaagatgatgacaatatttcttttgatttaattatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
atttaat putative branch site (score: 4)
atgacaatatttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtttttcttgtggtccttttttaaatgatctcaaaatttcatccataaagaagatgatgacaatatttcttttgatttaattatgttgctgtatatagGAACATTTGACAAAAGATGATGCAAGACAACAATTTCTAAGGATCTTGAGAACACTGCCTTATGGGAATTCGGTTTTCTTTAGTGTTCGCAAGATTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - -ttgtggt
- - - - - - - - - - - - - - - - tcaaaat
- - - - - - - - - - - - - - - - - - - - tcatcca
- - - - - - - - - - - - - - - - - - - - - - - -taaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgac