Sequence
atgc intronic sequence ATGC exonic sequence...cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
-------------------------------------------------------------------------cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|||| ||| | | | || ||| || || | ||| |||| |||| | | || | | | | |||| |||||||| ||||| |||||||||||||| ||||||| ||||||||||| ||||||||||||| || || ||||| ||||||||||| ||||| || ||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggc-ttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
-----cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| | |||| ||| | | | ||| | | | |||| || || | | ||| | | || | | || | | |||| |||||||||||||| ||||||||||||||| | || || |||||||| |||||||||| ||||| || || ||||| || || ||||| || || || ||||
atgccatgctcttgaactatcgatacatatgcttagcataccaatttgga--taatttcaaatgcact-tgcaccatactaaactcaaatgtgtt--ttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatat-----caaatttcttaaaaccttctccattttt-cagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| | || | | | || | | || | || ||||||| ||| | |||| ||| |||| || | | |||| |||||||||||||| ||||||||||||||| |||| || |||||||| ||| |||| ||||| || || || ||||| ||||| ||||| ||||| |||||||
----tacttgaacagtgtgtacatagtgtg-gagtttgatgtatcagcttgttttac-aaattttatagaatcacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G375975_T01 (Zea mays), 3'ss of exon 3
---------cttttgatgaaatatgacctct-ttggtttataaaatttaagtggagttatgttttattaaactatat-atcaaatttc-------ttaaaacctt---ctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
||| | | || ||| | | | | | || ||| || | | | | | | || | | |||| ||| ||| | || ||||| ||||| ||||||||||||||||| |||||| |||| || |||||||| |||||||||| ||| || || || ||||| || || ||||| || || || |||
gtcggatagttttcacccggacacaacttctactagctcttcattgctatatggttttttactgtttaagagtacaccacttcattttgctgaatttacaacttaacacttaattttgcagTATACTCCTGCGATTGATATCTGGAGCCTAGGTTGTATATTTGCTGAAATGCTTATAGGGAAGCCTCTCTTTCCTGGCAAGAATGTGGTACATCAACTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G05700.1 (Glycine max), 3'ss of exon 4
----------cttttgatgaaatatgacctctttggttta-taaaatttaag----tggagtta--tgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
||| | || || |||| |||| | || |||||||| || | || || | |||| || ||| || ||||| |||| | ||| |||| ||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| || || || || ||||||| ||||||||||| |||||||| ||||
gtaagtttcttcttttttttaacatcttttcttgggttgaatataatttaagcaattgaacatacttggtgtattgaaatatgcatgtaattt--taaatttatttcctttttgcagTACACTCCAGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G33980.1 (Glycine max), 3'ss of exon 4
--------cttttgatgaaatatgacctctttggtt-tataaaatttaagtgg--agttatgttt----tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
||||| | || || |||| |||| |||| ||| |||| ||| || |||| || ||| || ||||| |||| | ||| |||| |||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| || || || || ||||||| ||||||||||| |||||||| ||||
gtaagcttcttttcttttaacatattttcttgggttctatataatataagcaattgaacatgcttgatatattgaattatgcatgcaattt--taaatttatttcctttttgcagTACACCCCTGCAATTGATATTTGGAGCATTGGGTGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAAAATGTTGTGCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G30790.1 (Glycine max), 3'ss of exon 4
--cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttt---tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| || ||| | || ||| | | | | ||| ||| |||| |||| | | |||||| ||| |||| || |||| ||||| || ||||| ||||||||||||||||| ||||||||||||||||||||||| | || || || ||||||| || ||||||||||||||||| ||||
cctcttcaatcctcctctaccgggattgtgtatgatttatgaagttgaatatatttaagtattgcacta-gtgtgtaatttc--aaatccttgtc--ttttgcagTATACGCCTGCAATTGATATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
-cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttt---tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| || ||| | || ||| | | | | ||| ||| |||| | || | | ||||| ||| |||| || |||| ||||| || || || ||||| ||||||||||| ||||||||||||||||||||||| | || || || ||||||| || ||||||||||||||||| ||||
ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttc--aaatccttgtc--ttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
cttttgatgaaata-tgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccattttt-----cagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| ||| ||| | | | | ||| |||| || || | | | | |||| | || | | | || | | | | || || ||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| || || || || ||||||| ||||| ||||| |||||||| ||||
-gtaaaatgcaattctctattttcttttttgcaaaagttgtctg-attcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
cttttgatgaaatatgacct-ctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
| | || | | | ||| || | ||| | | ||||| | | || | || | ||| || ||| | | | ||||| || ||||||||||||||||||||| | || ||||||||||| |||||||| ||| || ||||| ||||| || |||||||| || ||||| ||||
ccacttttgtatgaaggcctgctctagttagctatctacaagtgt-gcaggataaggtttgattacagatctgatgctaactctacttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G18150.3 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------cttttgatgaaatatgacc---tctttggtttataaaatttaa--gtggagttatgttttattaaactatatatcaaatttcttaaa--------accttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| |||| | | | | ||| || ||| | ||| ||| | | | || | | || ||| || || | || |||||||| || |||||||||||||| ||||| | || ||||| ||||| ||||||||| || || || ||||||| |||||||| || |||||||| ||||
gtaagattctttttcaccaaacccaactactcttgctatttctccctaccaggaaaatgcttctagttttctattttgtagaatattgttgtgtggttctatagtgttgttgagaagaccagccatctcaagctaagtctactcttgttatatttcagTATACCCCTGCGATTGATATCTGGAGTGTCGGTTGCATTTTTGCGGAAATGCTTTTGGGTAAGCCTTTGTTTCCCGGGAAAAACGTTGTGCACCAATTGG
upper sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S80_71V6.2 (Physcomitrella patens), 3'ss of exon 4
----------------------cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
|| | |||| | | || || ||| | | | | | ||||| || | | | || | | | || | | ||||| ||||||||||| ||||| ||||| ||||| || |||||||| ||| || | || ||||| ||||| ||||| || || ||||| || || || |||
gtgagcagcactagtacccttcgttctattgaactttatgtactgtga--cgcaaattgttattaagaacacgtttt-ttgtgtggtgtgactaaataag-attatgttacttgtgctgcagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACTGGAAAGCCGCTTTTTCCTGGAAAGAATGTCGTTCATCAACTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
ccttctccatttttc CT-rich tract
ttttattaaactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttttattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -tgaaata
- - - - - - - tgacctc
- - - - - - - - - - - - - - -ataaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttaaaa