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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA

Basic information

species Arabidopsis thaliana
transcript AT5G20350.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 9
gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgat-gctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                           |   | ||   ||  |       ||  || | | | | |  ||||||     | |   ||||  |    | ||| ||  |||||| | |||||| ||||  | ||||| ||||| || |||||||| ||||| ||||| ||||| || || |||||||||||||| |||||  |||| || 
--------------------------gtaagtacagcattgtcgattagttttctctttgctaggttgatatttgggcctctgattccaaggg---ttattcta--cagATTGTGAGACCTGTTCGTTCGAAGCATTGTTCTACATGTGATCGCTGTGTTGAGCAGTTTGACCATCACTGTCCTTGGGTATCTAATTGCATTGGCAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G024437_T02 (Zea mays), 3'ss of exon 9
gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtcc-actgtgtttcat-tttatt-cagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                        ||   ||       | | ||    | |||||  ||  |  |  ||  ||| ||   | | ||  | |   | |||| || ||| |||||  |||||||| ||||  | || || ||||| || ||||||||||| || ||||| |||||||||||||| ||||||||||| |||||  | ||||| 
------------------------gtaagtcactcgattgagca----atttaattctctttctttgattgttattttcatagatcagatttcctatcatcttcattacagATAGTCAGACCTGTTCGTTCGAAACATTGTTCTACATGTGATCGTTGCGTGGAGCAGTTTGATCACCATTGCCCTTGGGTATCTAATTGCATAGGAAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G409934_T01 (Zea mays), 3'ss of exon 3
gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                     || || |||||| | |    |  |  |      ||  |     |    ||||   ||   ||| |   | ||  |  | ||| | ||||| |||| ||| | ||  | || || || || || || || || ||||| |||||||| ||||| || || |||||||||||||||||  ||||||| 
--------------------gtaagtttttctttattaagtaatctgtggggtttccccttaaattagcatttttctgaagtggcctcatttgcctagtattaat-agATTGTCAGGCCTGTACGCTCAAAACATTGCTCTACATGCGACCGCTGTGTTGAGCAATTCGATCATCACTGCCCTTGGGTATCAAATTGCATTGGAAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 9
---------------------------gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtc----cactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                            | | ||||  ||  | | |  ||||||| | |  |     | |    |  |     ||  | ||     || | ||||||||  |       | ||||   |||| |||||||| |||| ||||||||||| || |||||||||||||||||||||||||| || ||||||||||||||||||||||||||||| |||||  | || || 
gttctttgctttcttttgattgtctgacttcttgctgtaaagctgatcaatgtcttgcatacac----agattgcagatgccggtctttcctttgctttgaattgttttgcacacaattttatgttgtcttttcttcagATTGTCAGGCCTCTTCGAGCAAAACACTGTTCCACCTGTGATCGTTGTGTGGAACAATTTGATCACCATTGTCCTTGGGTATCCAATTGCATCGGCAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 10
---------------------------gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtc----cactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                            | | ||||  ||  | | |  ||||||| | |  |     | || | || |   ||||  | ||    ||| | ||||||    |       | |||| | |||| || ||||| |||| ||||||||||| || |||||||| |||||||||| |||||| || ||||||||||||||||||||||||||||| |||||  |||| || 
gttctttgctttctgttgattgtctgacttcttgctgtaaagctgatcaatgtcttgcatacac----agactacacatgcccatcttt-ctttgcattgaattgtttcatacacagttttatgttgccttttctttagATTGTCAGGCCTCTTCGAGCAAAACACTGTTCTACCTGTGATCATTGTGTGGAACAATTTGATCACCATTGTCCTTGGGTATCCAATTGCATTGGCAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 9
gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
|| |||  |  | ||| | ||| |||     ||      | ||    |    | |  || || ||| |  |   | || | || | | || |      | ||||| ||||| ||||||||||||| || ||||||||||||||||||||||| ||||| || || ||||| || ||||| |||||||| || |||||  |||| || 
gtgcctttt--acttctggtttttgttgccttttttgtatgacttgttcaacatttgtctattcta-acttcagcctgatgtgattc-ctattcgatttgttatt-agATTGTCAGACCTCTTCGTGCAAAGCACTGTTCCACCTGTGATCGATGTGTCGAACAGTTTGACCATCATTGCCCTTGGGTGTCTAATTGCATTGGCAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S70_186V6.2 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------------gtacctgctcaaattccgttttatgtctttcttca-atcttaacac-catacttaatcat-cgatgctacatatttacttgttttggtccactgtgtttcattt---tattca---gATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                                                      ||||| || |  ||  ||| ||| |||  |  | |   |   ||   |||||  |  |  | ||    |  | |   | |      ||  || ||     ||   | ||||   |||| | |||||  | ||| | ||||| || ||| | ||  | || ||||| || |||||||| || |||||||||||| | |||||||||||||| || 
gtttgtcagttcgattattcacctcattcgatttgatttcctaagttattagaaacctgttcga--tcaatttaatggcttcttgaatagagtgctacatgtacttctttgtgtgctggagtaagtcttgatatccctagccgttgggtcatggttgcttgttcaatagATTGTGAGACCATTGCGATCCAAGCATTGCTCCTCATGCAACCGCTGTGTCGATCAATTTGACCATCATTGTCCTTGGATTTCAAATTGTGTTGGCAAG

upper sequence: AT5G20350.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ29308 (Selaginella moellendorffii), 3'ss of exon 3
gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
                                              | ||| |||  | | |   |  | |||| | ||| ||  | | |   ||| ||    | |||||  | || ||| |  || | ||||||||||| |  ||  | || ||||||||||| || |||||||||||||||||| ||||||| |||||||| || 
--------------------------------------------gtagact-aatttttgctttcatct-tttagtcgttgtgagcaaat---ttttat----tgcagATAGTGAGGCCTGTAAGATCCAAGCACTGTTCGATTTGCAACCGCTGTGTAGAGCAGTTCGATCACCATTGTCCTTGGATATCAAACTGTGTTGGGAAG

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|164006077|gb|ES017261.1|ES017261
EST:     CTTTGCTTGCTGGGAATTGGACACAGCTCTGTACAACATGCAAG                         ATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGT
genomic: CTTTGCTTGCTGGGAATTGGACACAGCTCTGTGCAACATGCAAGgtacctgctc ... ttttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcatcgatgctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA
 acttaat  putative branch site (score: 4)
                                        tttcatttt  putative PPT
              atatttacttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctgctcaaattccgttttatgtctttcttcaatcttaacaccatacttaatcatcgatgctacatatttacttgttttggtccactgtgtttcattttattcagATTATCAGACCTCTTCGAGCTAAGCACTGTTCCACCTGTGATCGTTGTGTAGAGCAATTTGATCACCATTGTCCTTGGGTATCAAATTGTGTTGGAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA