Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag

Basic information

species Arabidopsis thaliana
transcript AT5G55160.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g68950.1 (Oryza sativa), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactc-tctgtaccccattctct-tttactgttttccgtttttca-aagttgtatgatttccttaaccgagaatcttc----aattttacag
 |||||||| || || ||||||||||||||||||||| | ||  | ||||| ||| | |||||||||||| | || |||| ||||||||| || || |||||  | |  ||  |||   |  ||| |||  || | | ||| | |    |   || |  |      ||| | || ||  | | |     | || | |||
GCTGATGAACGCCTATTGTGACCGTCAGTCTGTGGATATGAATGCTATTGCATTCCTATTTGATGGTCGTAGGCTCCGTGGCGAGCAGACCCCTGACGAGgtg-cgtagcttatcttctcttcatactcaattcagtatttgcggagcctagcaaatcatcaccaatccattactgatgaccattgcaaacttgttcag

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g68940.1 (Oryza sativa), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttt------------------tactgttttccgttt--ttcaaagttgta--tgat-ttccttaaccg----agaatcttcaattttacag
 |||||||| || |||||||| || ||||| |||||| |||| || ||||| ||| |||||||||||||| | ||   ||| |||||||| || ||  ||||  | | |    |  |||  | ||||||                    |||||  |||| |      ||  | | ||  ||||  |  || |||     | | | ||  |||| |   
GCTGATGAACGCCTACTGTGATCGCCAGTCCGTGGATATCAAATCTATTGCCTTCCTGTTTGATGGTCGTAGGCTCAATGCTGAGCAGACCCCTGACCAGgtg-cgtgatataccatactgccttctctaaacaatgagctgatgcaaatactgccttccctaaaacccagtgctatagctgatgcttttttaccactgcaaactgtttgatttcag--

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G082390_T01 (Zea mays), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag
 |||||||| ||||| |||||||| |||||||||||  | ||  | ||||| ||| |||||||||| ||  | ||||| | ||||||||| || |||||||| ||   | ||      |   |    |    | ||  |    |  || |  | |  ||  ||| | |   |                    
GCTGATGAACGCTTATTGTGACCGCCAGTCTGTGGACATGAATGCCATTGCGTTCCTGTTTGATGGCCGCAGGCTTCGCGGCGAGCAGACCCCTGATGAGgtgacccaattcg----gctttagatcccagcattgagtggaatacttgatcgatagatcttttgcctgtgcag------------------

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA08G46500.2 (Glycine max), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgat----ttccttaaccgagaatcttcaattttacag------
||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||||||||||||||||||  |  | || || || || ||||| || ||||||||||  |   | | |  |  || |   |     |   ||||   |||| |  | || |   |    |||  | ||   |   ||  | |||   ||      
ACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCTGAACAGACCCCTGATGAGgtaaatttggtttgttcaagccttgtacaaactcaagtttcatcttttaattgctgcaaagtacaattctgttactatg--cctatagtttggtagaattat

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA18G35450.1 (Glycine max), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttc--aattttacag------
||||||||| || |||||||| ||||| ||||| ||||| ||||||||||||||||||||||||||  |  | || || || || ||||| || ||||||||||  |   | |    |  || |   |     |   ||||   || | |  | ||     | |  ||     |  ||  |   | |||   ||      
ACTGATGAACGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTGCTTTCTTGTTTGATGGAAGGAGACTCCGAGCAGAACAGACCCCTGATGAGgtaaatttggtttggtcaagccttgtacaaactcaagtttcatcttataattgctgctaagtataattctgttactatgcttatagtttggtagaatttt

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0186g00020.t01 (Vitis vinifera), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatc----actctctgtacc--ccattctcttttactgtt--ttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag
 || |||  |||||| ||||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || || ||||  ||||||||||||||||||||||          | |||| |       ||  |  |   ||||  | ||     |     ||  |||  |   |  |  |      | |    | |  |
GCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTGCATTCTTATTTGATGGTCGCCGACTCCGTGGAGAGCAGACTCCAGATGAGgtaaggcttttggttttctgaattatttgttggccatccatgttgctcccccacctgtggcttccatgcatatttctataggtggaatgcgggatgatgg

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv00s0186g00080.t01 (Vitis vinifera), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcact--ctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag------
 || |||  |||||||||||| |||||||| ||||| || ||||| ||||| ||||| ||||||||||| || || ||||  ||||||||||||||||||||||      |   | | |     |||   |   | |   |   | ||  ||    ||  |   |    ||       ||   || || || ||      
GCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTGCATTCTTATTTGATGGTCGCCGACTCCGTGGAGAGCAGACTCCAGATGAGgtaaggcttttggttttctgaattatttgttggcaatccatgttgcttcccacctgtggcttcctgttgtatgtatacatgcacatttctataggtggaa

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv12s0059g01310.t01 (Vitis vinifera), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctctttt----actgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag
 || ||||||||||| |||||||| || ||||| ||  ||||||| ||||| ||||||||||||||||||||||| || |  || || || || ||||||||| |       | |  | |  || ||    |    |     | ||   || |   | ||  ||||    ||| |      || |    || ||||
GCTCATGAATGCTTATTGTGACCGACAATCTGTAGACCTCAACTCGATTGCATTCTTGTTTGATGGTCGTCGTCTCCGGGGAGAACAAACCCCTGATGAGgtatctctctcattttaatcttatccttgagttggaatccaatgccccattgcctggatgcctgatgcttttatctt----tcctttgcttcacag

upper sequence: AT5G55160.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S61_57V6.1 (Physcomitrella patens), 5'ss of exon 2
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcact----ctctgtaccccattctcttttactgttttcc---gtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag-
 |||||||| |||||||||||||| ||||||||||||     ||| ||||| ||| | ||||| || ||||||||||| || || ||||| || | |||||||    |       || |||    ||||| |    || |   |     |    | |   ||  |    ||| | | | || | || | ||     ||  
GCTGATGAACGCTTACTGTGACCGCCAGTCTGTGGATCCTTCCTCTATTGCATTCCTCTTTGACGGCCGTCGTCTTCGAGCTGAACAGACACCTGCTGAGgtattcccttcaaagctttgttttgcattcgccaaaacagaaataaaaagaacattacctttaaaacggttcttcagctgaaattcctgaagacatcaac

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|152038446|gb|AV823309.2|AV823309
EST:     CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGT
genomic: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGT
EST: gi|86076387|gb|DR372144.1|DR372144
EST:     CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGT
genomic: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGT
EST: gi|116456891|gb|EG499483.1|EG499483
EST:     CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTG
genomic: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTG
EST: gi|163966477|gb|ES185369.1|ES185369
EST:     CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAAT
genomic: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAAT
EST: gi|164126265|gb|ES092834.1|ES092834
EST:     ATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCA
genomic: ATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCA
EST: gi|86082102|gb|DR377861.1|DR377861
EST:     CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGT
genomic: CTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGGT
EST: gi|163979819|gb|ES135192.1|ES135192
EST:     CGTCGTCTTCGTGCCGAGCAGACTCCAGATGAG                         CTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGG
genomic: CGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcac ... aattttacagCTTGAAATGGAAGATGGAGATGAGATCGATGCAATGCTTCATCAGACTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTGCTTTCTTGTTTGATGGTCGTCGTCTTCGTGCCGAGCAGACTCCAGATGAGgtaacatcactctctgtaccccattctcttttactgttttccgtttttcaaagttgtatgatttccttaaccgagaatcttcaattttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG