Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G23325.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os08g34480.1 (Oryza sativa), 3'ss of exon 2
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgg-gaacaatttgctttagttcttgtaaag---gttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
| || | |||| || | || ||| | | | | |||| || | |||| | || | | | |||| | ||| || || | |||| || || ||||| |||||||||||||| ||||||||||||||||| || ||||| || ||||| ||||| || |||| ||||
---------------------------------------------------------------------------------tttattcagtttaaatatgttgtaccttttcaatgaactttggtaatatccttttgtattttgaccatgatgttgatatgataaatcatcttctt-------taaagGCTAGCGACAGGTTCAACATAAATTCTCAACTTGAGCATCTTCAAGCGAAATATGTGGGCACAGGGCATGCTGACTTGAATCGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagc----agatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
|||| | | | ||| | | | | | | | |||| | | | |||||||| || | | | || | | || ||| | ||| |||| || |||||||| |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| |||||| |||||
---------------------------------------------------------------------------ttaa---aggttcaactggatcttag------tcttcagt-gttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---agGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagc----agatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
| | || |||| | | |||| | | | |||||||| || | | | || | | || ||| | ||| |||| || |||||||| |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| |||||| |||||
----------------------------------------------------------------------------------------ggttcaa--ctggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaa---aggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G106574_T01 (Zea mays), 3'ss of exon 2
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttt-tttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
| | ||| || |||| | | |||| | || | ||||||| || | | ||| || ||| || | |||| || ||||| || |||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| |||||| |||||
-----------------------------------------------------------------------------------actttggctcaa--ctggatcttagtcttcactgttcattcaatagctaggtttgctgacattttgaggacaatatttctaacacaatttaccattttaaagGCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G40200.1 (Glycine max), 3'ss of exon 1
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
|| | |||||| || | || || || | | ||||| |||| || || | | | ||| | |||| | ||||| ||||||||||||||||| ||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||||| ||||||
-----------------------------------------------------------------------------gtacttttcagtttctcaatctgtgacctatgtgaattggagtt------aattagggtttt------caaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G40200.2 (Glycine max), 3'ss of exon 1
--------gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttct-tgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaa-ggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
| || | | | ||||| || || | | ||| |||| | |||| | || ||||| | | | | | | | | | || | ||| | ||||| |||| || || | | | ||| | |||| | ||||| ||||||||||||||||| ||||| |||||||||||||| ||||| || |||||||| || || ||||| ||||||| ||||||
gtagagattctattcccaatttccttgaaacgctctttccctctttccgttc--actcgctccgttatgaagttcaggctgcgattcaattttgtacttttcagtttctcaatctgtgacctatgtgaattggagttaattagggtttt------caaattcggtcccgaattgagtttgtgcgttttatacagGCCAGTGATAGGTTTAACATCAATTCCCAGCTTGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCCGATTTGAACAGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G17590.1 (Glycine max), 3'ss of exon 1
------------gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgta---atctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
| || | | || ||||| || || | | ||| ||| | | | | ||| || | | | | | || | | | | | | || | ||| || || | ||| | | | || || | | | ||| | |||| || |||| ||||||||||||||||| ||||||||||| |||||||| ||||| || |||||||| || || ||||| ||||||| ||||||
gtagagagaaactctattcccaatttctttgaaacgctcttttcctctttccattc--acttgttctgttacgaaaacttcaggc---tgggatacaatttctttatttttcagtttctcaatctgtgacctatgtgaactggagttaattagggtttttaaatttggatacagaaatgaatttgtgagttttatgtagGCTAGTGATAGGTTTAACATCAATTCTCAGCTCGAGCATCTCCAAGCCAAATATGTTGGAACTGGCCATGCTGATTTGAACAGATT
upper sequence: AT3G23325.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv05s0049g01230.t01 (Vitis vinifera), 3'ss of exon 1
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
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---------------------------------------------------------------------------------tgtgtgtag-tattttttatttttgaaatactttgaattgtgtcaagcacttatccatgttta-cttgtaattg-ataaacattgtcatctgtaattgcacagGCCAGTGATAGGTTTAATATTAACTCCCAGCTTGAGCATCTGCAAGCAAAATATGTTGGAACTGGTCATGCTGACTTGAATAGATTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124823590|gb|EH908456.1|EH908456EST: ATTCTTCTTCTTGCGAACTCGCTGAAGTCTGAAAGATGCAG GCAAGTGATAGGTTTAACATAAATTCT
genomic: ATTCTTCTTCTTGCGAACTCGCTGAAGTCTGAAAGATGCAGgtttgtctct ... ttttgtgcagGCAAGTGATAGGTTTAACATAAATTCT
EST:
gi|164171336|gb|ES065072.1|ES065072EST: ATTCTTCTTCTTGCGAACTCGCTGAAGTCTGAAAGATG-AG GCAAGTGATAGGTTTAACATAAATTC
genomic: ATTCTTCTTCTTGCGAACTCGCTGAAGTCTGAAAGATGCAGgtttgtctct ... ttttgtgcagGCAAGTGATAGGTTTAACATAAATTC
EST:
gi|164202343|gb|ES134671.1|ES134671EST: ATTCTTCTTCTTGCGAACTCGCTGAAGTCTGAAAGATG-AG GCAAGTGATAGGTTTAACATAAATTCTC
genomic: ATTCTTCTTCTTGCGAACTCGCTGAAGTCTGAAAGATGCAGgtttgtctct ... ttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
atctcac putative branch site (score: 3)
tctcacttttttgttt CT-rich tract
acttttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctctctcgattcgaaaccctagttacttttttttgttcttatctctaattttatacaatttcttgacgattaagctaagcgtagctgaaatctgggaacaatttgctttagttcttgtaaaggttaggtttttaagcagcagatagttatgtaatctcacttttttgtttttgtgcagGCAAGTGATAGGTTTAACATAAATTCTCAGCTTGAGCATCTTCAAGCTAAGTATGTTGGTACAGGTCATGCAGATTTGAGCAGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT