Sequence
atgc intronic sequence ATGC exonic sequence...cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g68010.1 (Oryza sativa), 3'ss of exon 4
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacattttt---------agGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
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---gttctagtacgc----gcaccctatgtttgtatttttcaccagcttgca-tcattc-tgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAG
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g68010.5 (Oryza sativa), 3'ss of exon 2
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacattttt---------agGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG-
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---gttctagtacgc----gcaccctatgtttgtatttttcaccagcttgca-tcattc-tgatgttactactaatttatatcagctttgacatatatctttcgtgcagTATTCAGAGATTATCGAGCAAATTGACCGTGATGTGAAGCGCACTCACCCTGACATGCATTTTTTCTGTGGAGACTCATCTTTTGCAAAGTCCAATCAGG
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G36520.1 (Glycine max), 3'ss of exon 4
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttga-attatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
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-----------gttctact----tctatctctatgctatgctatcacctac--ttgcaaacacatttctgccactctttctttca--ttg-----ttttagGACACAGAGATCATAGAGCAGATTGACCGAGATGTCAAGCGTACTCATCCAGATATAGACTTCTTCTCTGGTGATTCTCATTTTGCAAAATCTAATCAG
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G00430.2 (Glycine max), 3'ss of exon 4
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
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-------------------gtactactatctc-tattatgctatcacctac--ttacaacacacactttatgcctctctttctttctttg----tcttagGACACAGAGATCATAGACCAGATTGACCGAGATGTCAATCGTACTCATCCAGATATACACTTCTTCTCTGGTGATTCTCTTTTTGCAAAATCTAATCAG
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G11760.1 (Glycine max), 3'ss of exon 4
cccatttctttatgctattggactataaat-tggtattaggagatgata-tatggtcactgatgg-tgttttgaattatttattacaatttgaacatttt-tagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
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tccattattgtatcacaatta--tataaatctcatgctaatgcactataatactctgtgcaatggctgttgtgaagcaa--atttccgtctttgcattttgtagGATACAGAGATCATAGATCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G28660.1 (Glycine max), 3'ss of exon 4
cccatttctttatgctattggactataaat----tggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
|||| | ||| | | ||||||| || || | || ||| || | | | |||| |||| | | | |||| | ||| ||||| ||||||||||| || ||||||||||||||||| |||||||||||||| || ||| |||| |||||||| || | | || ||||||| | ||||||
ttcattattgtatcacaatta--tataaatctcatgctaatgccctataatactctgt-gcaaaggctgttgtgaagcaaatctccttctttgcat-tttgtagGATACAGAGATCATCGACCAAATTGACCGAGATGTAAAGCGCACTCATCCTGATATGCACTTTTTCTCTGGTGATTCCCAATTTGCAAAATCTAATCAG
upper sequence: Vv05s0029g01350.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G04830.2 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------cccatttctttatg------ctattggactataaattggtattaggagatgatatatggtcactgatg-gtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
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gtactatatcttacatcctgggcaggtctttcattgtcttaatcttttagagagacctcagtgcattacttaaggacaggattaaaggttatatagtatttaatttgtccactagttccatcatcactcttttgttaatgt-agGATACGGAGACCATAGAACAAATAGACAGAGATGTCAAGCGTACACATCCAGACATACCCTTTTTCTCCGGTGAATCATCGTTTGCGCGTTCTAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatggtcactgatggtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
cactgat putative branch site (score: 3)
cattttt putative PPT
tgttttgaattattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cccatttctttatgctattggactataaattggtattaggagatgatatatggtcactgatggtgttttgaattatttattacaatttgaacatttttagGACACAGAGATCATAGAGCAAATTGACCGAGATGTCAAGCGCACTCATCCAGACATGAACTTCTTCTCTGGGGACACGCCATCTGCAAAAACAAATCAG
-ccatttc
- - - - - - - ctattgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatggtg