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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgcctttttatcttaaatttagattcttttcccttagttatgtgttttaacattcatatgctgtttgctgcgatcccttagttatatatgtgttcat...

Basic information

species Arabidopsis thaliana
transcript AT4G32690.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G32690.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G155868_T01 (Zea mays), 5'ss of exon 2
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgt----ttgcctttttatcttaaatttagattcttttcccttagttatgtgttttaacattcatatgctgt-ttgctgcgatcccttagttatatatgtgttcat
   |||||       || || || || ||||||||||| ||||||||||||||| |  ||||||| ||||| ||||| ||| | |  || ||||| | ||||    | |||  | | ||||    || ||    |  ||    |   |    ||        | ||   |  |   |||  |    |||||   | |  |     
GAGATATTCGGGGGGTCGAAGAAGGAGGATGCCATCCAGAACCAGTATGAGTTCCTGATCCAGCGCATGGGCGGCCCACCTCTATTCTCCCAGAGGAGAGgtaaagtagcccgtgtttcttcgtctttgacctgtggcctgcgggacttaaattaggggaggaaataagggatcaatgctgttatatagtttggtcttag-----

upper sequence: AT4G32690.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA14G20380.1 (Glycine max), 5'ss of exon 2
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgcctttttatcttaaatttagattcttttccctta-gttatgtgttttaacattcatatgctgtttgctgcgatcccttagttatatatgtgttcat-
||||||||  | || ||| | || ||  ||||||| |||||||| || |||||||| || ||||| ||||| || |||||| | | ||||||||||| ||||   | ||||| |  | | |  | ||  ||     |||   ||  |  | |||        ||    ||    | |||  |     ||  ||   | ||| 
TCAATATTCGCGAATTCTGAGAAGGAGAATGCCATTCAAAACCAATACGAGTTCTTCGTGCAGCGAATGGGTGGTCCTCCTCTCTTTTCTCAGAGAAGAGgta-acatttttttgctgactcgaaatatttccaatttacagtagatagtgtaattgctccgtgaaaattataac-atctttagtgcatgcatagatacata

upper sequence: AT4G32690.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv04s0008g04210.t01 (Vitis vinifera), 5'ss of exon 2
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttg------cctttttatct-taaatttagattcttttcccttagttatgtgttttaacattcatatgctgtttgctgcgatcccttagttatatatgtgttcat
|  || ||| |||| ||||| |||||||| || || || || || |||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||||  |        | ||| | | |  ||  | || || |||      | |  |  |||    |  | ||  ||  ||     ||| |  | | | | |  |      
TTGATTTTTGCTAATTCTAAGAAAGAAGAAGCAATTCAGAATCAATATGAGTTCTTTGTACAGCGAATGGGAGGGCCCCCTTTATATTCCCAAAGGAAAGgtaaggagcaatttatttgtttatttatgaaaatgctattcttcgcatcaaattcttttgactctagattgtgactgggatcatcaca-aatcagaaaaat------

upper sequence: AT4G32690.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S309_63V6.1 (Physcomitrella patens), 5'ss of exon 2
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgcctttttatcttaaatttagattcttttcccttagttatgtgt--tttaacattcatatgctgtttgctgcgatccctt-agttatatatgtgttcat---------------------------------------------------------------------------------
||||||||| | || ||||  ||||| |||||||| ||||||||||||||||| ||  | ||||| ||||| || || ||| | ||  | || |||||||||      |      | ||      |||| | ||  ||   | || ||  || |   |  ||  |   |    | |  ||  || ||   | |   ||    |                                                                                 
TCAATATTTGCAAATTCTACTAAAGATGATGCCATTCAAAACCAGTATGAGTTTTTCATTCAGCGAATGGGTGGACCACCTCTTTACGCCCATAGAAAAGgtacatactcaccgatcaatcacttattcctctcatttgtgtgtgggtcattcattgtagattcgtcatggaatactctcgtttgagcagtctgcttgaaagtcattcaaattgatctctcttgaaatcttcgaatcacaactcagcgagcaatttatgtaactgcttgaattcttcacggcag

upper sequence: AT4G32690.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ07410 (Selaginella moellendorffii), 5'ss of exon 2
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgcctttttatcttaaatttagattcttttcccttagttatg--tgttttaa--cattcatatgctgtttgctgc---gatcccttagttatatatgtgttcat------------------------------------------------------------------------------
|| || ||| | || ||   ||| || |  |||||||| |||||||| ||||| ||  ||||| | |||||||||||||| || |||||||   | |||||| |||  |    ||||     |   || || ||  ||| || |   | | || |  | |||   || | ||| || |   | | |||   ||   |  || ||| |                                                                              
TCGATCTTTGCGAATTCCTCCAAGGACGCCGCCATCCAGAACCAGTACGAGTTTTTCATCCAGAGAATGGGAGGCCCTCCATTATATTCTCGTCGCAAAGgtatgcaatgcgttctttttcctccttttttctcgtttatttcttcttctcttgagtcgttctcttgttctttccttctccgcttcctctctttctttcgtcttccttgacttttccatcgttctcattttgttttagcatttctcatttgagtttttaaaattttctcacgaccaaacttacag

upper sequence: AT4G32690.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: EFJ19882 (Selaginella moellendorffii), 5'ss of exon 2
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgcctttttatcttaaatttagattcttttcccttagttatgtgtttt----aacattcatatgctgtttgctgc---gatcccttagttatatatgtgttcat------------------------------------------------------------------------------
|| || ||| | || ||   ||| || |  |||||||| |||||||| ||||| ||  ||||| | |||||||||||||| || |||||||   | |||||| |||  |    ||||     |   || || ||  ||| || |   | |       | |||   || | ||| || |   | | |||   ||   |  || ||| |                                                                              
TCGATCTTTGCGAATTCCTCCAAGGACGCCGCCATCCAGAACCAGTACGAGTTTTTCATCCAGAGAATGGGAGGCCCTCCATTATATTCTCGTCGCAAAGgtatgcaatgcgttctttttcctccttttttctcgtttatttcttcttctcctgagtcgttctcttgttctttccttctccgcttcctctctttctttcgtcttccttgacttttccatcgttctcattttgttttagcatttctcatttgagtttttaaaattttctcacgaccaaacttacag

Mapped 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|116438119|gb|EG480711.1|EG480711
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438120|gb|EG480712.1|EG480712
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438101|gb|EG480693.1|EG480693
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438051|gb|EG480643.1|EG480643
EST:     GTTCTTTGTCCGGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|86051380|gb|DR347135.1|DR347135
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTCCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438082|gb|EG480674.1|EG480674
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|86051381|gb|DR347136.1|DR347136
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|19797232|gb|AU229158.1|AU229158
EST:     TTGTCCAGCGTAT-GGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCCGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: TTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438011|gb|EG480603.1|EG480603
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTTTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCCCCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|86051379|gb|DR347134.1|DR347134
EST:     GTTCTTTGTCSAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTC
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTC
EST: gi|116438080|gb|EG480672.1|EG480672
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTTTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438049|gb|EG480641.1|EG480641
EST:     GTTCTTTGTCCGGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCCCCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116473420|gb|EG516012.1|EG516012
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438100|gb|EG480692.1|EG480692
EST:     GTTTTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTTTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCCCCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116473442|gb|EG516034.1|EG516034
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|116438012|gb|EG480604.1|EG480604
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
EST: gi|19877196|gb|AU238027.1|AU238027
EST:     GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAG                         GTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG
genomic: GTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgccttt ... caatgtgtagGTCATCCTGCTTTGATCGGACGTCACCGTCCATTTCCAGTGACCCATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAATATTTTCTAACTCTAACAAAGAAGATGCCATCCAAAACCAGTATGAGTTCTTTGTCCAGCGTATGGGAGGCCCTCCTTTGTATTCTCAGAGAAAAGgtttgcctttttatcttaaatttagattcttttcccttagttatgtgttttaacattcatatgctgtttgctgcgatcccttagttatatatgtgttcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgatccct