Sequence
atgc intronic sequence ATGC exonic sequencegtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os07g04210.1 (Oryza sativa), 3'ss of exon 11
-----------gtaaatctgaaaatctacag---ttccattggcttgtca-ataccaaaaatt-tcattttatattcctttttttttccttttaatttctcaat--aatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
|| || ||| ||| |||| | | | ||| || | || | ||| || ||| | | || || ||| | | | | | | |||| | | ||||||||| | || ||||||||||||||||||| ||||||||||||||||||| | |||||||| || | || ||||| |||||||| || |||||||| |
gtaaggttgattcctgcttgtgtgccttcagcccttcatttggttcattacatagcagagcttgccctttcatgttcatgagccgattctatttattgccaatttgacttctctccattgtttgccct-tccagATTGCACTTGGTAATATTTTGAAGTTCCGAAGGAAGAATTGGCAGTTTGATGTGATTGGTGGTTTTGTGTACTTTGTTTTGGTTTTCTCGATGTTTCCGC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os07g01540.1 (Oryza sativa), 3'ss of exon 11
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcatt---ttatattcctttttttttccttttaatttctcaataatatggtgt-attggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
| || ||| | || | || | | | | | | | ||| | ||| | | || | || | ||||| | | || | | | ||||||||||| |||| ||||| | |||||||| |||||||||||||||||||| |||||||| |||| || || || |||| || || ||||| ||||
----gtatgttgttctctatgataatggaatttctgaaatttatagcctaactagcttaagtagcttgtatgttgtgtacaagtga--aataaggaaatcttatcaattaaat-atgcagATTGCGCTGGGTAATATACTAAAGTTCCGCAAGAAGAATTGGCAGTTTGACACAATTGGTGGTTTTATCTACTTCATACTGGTATTCTCAATGTTCCCAC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G018356_T02 (Zea mays), 3'ss of exon 7
-----gtaaatctgaaaatctaca-gttccattggcttgtca----ataccaaaaatttcattttatattcctttttttttccttttaatttctcaataata-tggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
|| ||| | | || | | ||| | | | | || | | | ||| || || | | ||| || || | || | | | | | | |||||| | |||||||| | || ||||||||||||||||||| ||| |||||||| |||||| | |||||||| || | || ||||| |||||||| || ||||||||||
gtaaggttgatccgtacatttttatgttattctagttcattgcatggctgcatagcctgcgtttgatggtcatgatgtttggtttgtattatcatgtgacttctcttctttcattcattt--tctagATTGCACTTGGTAATATTTTGAAGTTCCGAAGGAAAAATTGGCAATTTGATGTAATTGGTGGTTTTGTGTACTTTGTCTTGGTTTTCTCAATGTTTCCAC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G135839_T01 (Zea mays), 3'ss of exon 11
----gtaaatctgaaaatc--tacagttccattggcttgtcaataccaaaaatttcattttatattcctttttt--tttccttttaatttctcaataa-tatggtgtattggtcatttgat--gcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
|| | | | | ||| | |||| | | || || || | || || | | | | | | |||| || | | | | | | | | | || |||||||||||||| || || ||||||||||| || ||||||||||||||||| ||||||| || ||||||| || | ||||| ||||| ||||| ||||
gtatgttttttcctatgttgatgaagtaattcttgcttatttagttcagtgatcagtttatgaatcttttgtgtactataccatcaattgtgagatgagcacgatctgat--ttactaaattcacagATTGCATTGGGTAACATATTGAAGTTCCGCAAAAAGAATTGGCAGTTTGACATCATTGGCGGTTTTATATACTTCATTTTGGTGTTTTCAATGTTCCCAC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G08860.1 (Glycine max), 3'ss of exon 10
gtaaatctgaaaatctacagttcc--attg-gcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtc----atttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
||| | ||| || || | || | ||| ||| || | | | | | | | || |||||| || | | | | | ||||||||| | |||||||||||||||||||||||||||| || || || || |||||||| ||||| |||||||| |||||||||||||||||||||||| | || ||||| ||||||||||
gtatg-cagaatatttataattgcttattatacttctccttctcttacttgtaagcactaaatcattttttcttaaatattttactagcacattatggtgtaacatttttaaatttgatgcagATTGCATTGGGAAATATCTTAAAATTTCGGAAGAAGAACTGGCAATTTGATTTTATTGGTGGCATTATATATTTTGTACTAGTCTTTTCAATGTTTCCAC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G36310.1 (Glycine max), 3'ss of exon 10
------------gtaaatctgaaaat--ctacagttc-cattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtca-tttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
|| ||| | || ||||| | || ||| || | || || ||| | | | | | || | | | | |||| | | ||||||||||||||||||||||||||| | || || || || ||||| ||||| |||||||| |||||||||||||||||||||||||| || ||||| |||||||||
ggtatgtagaatgtcaattaattgcttattatagttctccttctcttacttgtaagcacaaaatcgctttttttaaaaaaaaatattttactagcacgttatggttgtaacatatttttaaatttgatgcaGATTGCATTGGGAAATATCCTAAAATTTCGGAAAAAGAACTGGCAATTTGATTTTATTGGTGGCATTATATATTTTGTATTAGTCTTTTCAATGTTTCCA-
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G11800.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
| | || | | ||| || | || | | ||||| | | || || || | ||||||| || | || |||||||||| ||||||||||||||||| ||||| || ||||| ||||| ||||||||||||||||| |||||||| ||| | ||||| ||||| |||| || |
------------------------gtaagtttcctatcagtaaa--ttgccttgttttcagcttttcatagcattcggat------attaaatggtgttttctgctgtt--tgcagATTGCTTTGGGAAATATTTTGAAATTCCGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGTATTATATACTTTATCTTGGTCTTTTCGTTGTTCCCTC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G23000.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
|| | || | | || | | | | | || | | | || ||| |||| ||| || |||| ||| | | || |||||||||| ||||||||||||| |||||| | || ||||| ||||| |||||||||||||||||||| ||||| ||| | ||||| ||||| |||| || |
--------------gtaaactttttcttgtttcttgaacctcttatccacggttactgattcgccttcttttctttgcattctgatattttatgttgttt--gctgttatttgcagATTGCTCTGGGAAATATTTTAAAGTTCAGGAAAAAGAACTGGCAATTTGATTTCATTGGTGGCATCATATACTTTCTCTTGGTCTTTTCCTTGTTCCCTC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S72_100V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtat-tggtca--tttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
| || ||||| | |||| ||| | ||| ||| || | | | || | || | | ||| | |||| | |||| | || | |||||||||| |||||| || |||||||| |||||||||||||||| |||||| | |||||||| || |||| ||| |||||||||| || ||||| ||||
----gtatgtaaatc----ataacatt--cttcaaattactcaaatttatgcctgtctaggacatgatattggacaaagcttatgagtaaatttgtgtgtatggttaccttccttacagATTGCATGGGGAAACATCTTGAAGTTTCGAAAGAAGAATTGGCGTTTTGATGTAATTGGTGGTGTTGTATACTTTATATTGGTTTTCTCAATGTTCCCAC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S147_29V6.1 (Physcomitrella patens), 3'ss of exon 10
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtca-----tttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
| ||| || | || | | || | |||| | | | | ||| | | | | | || | || | ||| || |||| |||||||| || ||||| || ||| ||| |||||||||||| |||||| | |||||||| ||| | || ||||| || || ||||| ||||||||||
---------------------tatattattttttaaaaaaaagaagctaagttttgaaagataagtaatctgatttggaggtgtttgaactgatttgaactgattgaaatgttttatatagATAGCATTGGGCAACATTTTAAAATTCAGAAGGAAGAATTGGCAATTTGATGTTATTGGTGGTATTGTGTACTTTGTGTTAGTGTTTTCAATGTTTCCAC
upper sequence: Vv18s0001g11060.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ24167 (Selaginella moellendorffii), 3'ss of exon 10
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattccttttt--ttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
||| || |||| | | | ||||||| | | | | || | | | || | ||||||||||||||||| ||| ||||||| |||||||| || ||| |||||| ||||||| || || | ||||| || | |||||||| |||||||| |
-------------------------------------------------------gtatcccgttttggtgcttttcttaatttgtttctcctttc-tgactcgtgctctt--ttcagATTGCATTGGGAAACATTCTGAAGTTTCGAAAGAAAAACTGGAGATTTGATATCATTGGAGGAGTTTTGTATTTCGTCCTCGTTTTTTCCATGTTTCCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
tttttccttttaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatctgaaaatctacagttccattggcttgtcaataccaaaaatttcattttatattcctttttttttccttttaatttctcaataatatggtgtattggtcatttgatgcagATTGCATTGGGAAATATTTTGAAGTTCCGAAAGAAGAATTGGCAGTTTGATTTCATTGGTGGCATTATATATTTTGTATTGGTTTTTTCTATGTTTCCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG