Sequence
atgc intronic sequence ATGC exonic sequencegtattttaactactcaaaacaatctctatatcttcatgacattcaaagctggaacatgagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21030.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G17590.1 (Glycine max), 3'ss of exon 1
gtattttaactactcaaaacaatctctatatcttcatgacattcaaagctggaacat------gagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
| | ||| || | || | | | | || | || | | || | || | ||| ||| || || | | | | |||||| |||||||||||| ||||| |||||||||||| | ||||||||||||| || |||| ||| | || |||||||| || ||||||||||| ||||||
--aatataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
upper sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA16G08070.1 (Glycine max), 3'ss of exon 3
gtattttaactactcaaaacaatctctatatcttcatgacattcaaagctggaacat------gagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
| ||| || | || | | | | || | || | | || | || | ||| ||| || || | | | | |||||| |||||||||||| ||||| |||||||||||| | ||||||||||||| || |||| ||| | || |||||||| || ||||||||||| ||||||
--catataaatattaaacaaagcatatgggatttttagtttttgagaacttaattatcctgtaggagcaaagactgacaatacttagcatttgaatttgaa-gCCGAGAGATGTTTAATAAATGGCAAGCTCAAAGATGGTGGGGTGAGAATTACGACAGAATCATGGAACTTTACAACGTCCAGAGATTTAATAAACAAGCT
upper sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA09G34600.1 (Glycine max), 3'ss of exon 3
---gtattttaactactc--aaaacaatctctatatcttcatgacattcaaagctggaacatgagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
|||| || | | | | | | | | | | | | || | | | ||| ||| ||| | || | | | | |||||| |||||||||| | | | ||||||||||||||| ||||||||||||| ||||||| ||| | || |||||||| || |||||||| || || ||||||
tctttattgagaccatttgtatatgagaattttagttgttgaaaaagttaattatccagtaggag-caaagacttataatagttagcatttacatttgaa-gCCGAGAGATTTTCGACAAGTGGCAAGCTCAAAAATGGTGGGGTGAGAATTATGACAGAATCATGGAACTTTACAACGTGCAGAGATTCAATCGACAAGCT
upper sequence: AT2G21030.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv02s0033g00590.t01 (Vitis vinifera), 3'ss of exon 2
gtattttaactactcaaaac----aatctctatatcttcatgacattcaaagctggaacatgagataaaaactaaccattacttgtg-tcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
| | || ||| | ||| || | | | || || | | ||| ||| | ||| | | || |||||| ||||||| ||||| ||||||||||| || ||||||| ||||| |||||| |||| | ||||| |||||||| |||||||| ||||||||||||
-tttcatagaaactgggactttggggcctcaatttgcttgaaatatcttgagattttttgttgtg-gaaacttaattagcttttgggattccaaatttgaagCCGGGAGATGTTTAATAAATGGCAAGCTCAGCGATGGTGGGGAGAGAATTATGACCGGATCATGGAGCTGTACAATGTCCAGAGATTCAACCGCCAAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaagctggaacatgagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
aactaac putative branch site (score: 1)
tcttgtttt putative PPT
ataaaaactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattttaactactcaaaacaatctctatatcttcatgacattcaaagctggaacatgagataaaaactaaccattacttgtgtcttgttttgaaagCCGAGAGATGTACAATAAGTGGCAAGCTCAACGGCGGTGGGGTGAGAACTATGACAAGATCGTTGAGCTTTACAATGTACAGAGATTTAACCGCCAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT