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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG

Basic information

species Arabidopsis thaliana
transcript AT4G09800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G062911_T01 (Zea mays), 3'ss of exon 1
aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                    |  | |  |      |      ||| ||      |   |    |||  ||           | ||   |||  | || |||| ||| ||||    ||||| ||||| ||||| || ||| || | || || || || ||||| ||||||||||| ||||||||||| ||||| ||||| |
--------------------gtaagagctcctccctaccccattttgtcatcacggg-tcggcgattagtctgacacgcggt-tggcattggctttgcagTCGCTGATTGCGGGGGAGGACTTTCAGCACATCCTGCGTTTGCTTAACACCAACGTGGATGGCAAGCAGAAGATCATGTTTGCCCTCACCTCCATCAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G30730.1 (Glycine max), 3'ss of exon 1
aatgtaatcgcgagtaa-gttgataaattttgcgttttttttgtttagtttatgtgaaattactgatgggtt--aattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
   | ||||  || |   |    | | | |||  ||   | |||  |  || ||      || |  ||| ||  || ||| |  |   |   |  || | ||||| ||||| ||||| ||||| || || ||||| |||||||| ||||| || || || ||||| ||||||||||| ||||| || |||||||| |||||||
---gaaatcaagatttttgaaactgactcttgttttggatatgtaaaaattgtgcatttgtaattttggtttgaaactgattgatccttgtcttgttttatagTCGCTGGTGGCAAACGAGGATTTCCAGCACATACTTCGTGTTTTGAACACGAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTTACCTCAATCAAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G08690.1 (Glycine max), 3'ss of exon 1
-------------------------------------aatgtaatcgcgagtaagttgataaatttt---gcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                                     || |      | |   | | | |  || ||   ||  |||          ||| | ||    |  |  |||   | |   |||||   | |||     |  |||||||||| || || ||||| || || |||||||| |||||| |||| || || || ||||| ||||||||||| ||||| || || |||||||||||||
gtacgatttcagcgtttccgaattgattttgataaacaaagattcttcaaaagattcgttttatcttttggcaatttcaaaaggcgatttttttggctctgtttttggaggagtcacattttaaatggttttgcttacagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTAGATGGGAAGCAGAAGATAATGTTCGCTCTCACCTCTATCAAAG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G30970.1 (Glycine max), 3'ss of exon 1
-----------------------aatgtaatcgcga-gtaagttgataaattttgcgttttttttgtttagtttatgtgaaattactga---tgggttaattgaattttgtgttgt-tgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                         |   | ||||| || | |||| |||      | ||  ||||   |     |      | |||||   ||  ||  |||  | ||||| ||| |  |  || |||||||||| || || ||||| || || |||||||| |||||| |||| || || || ||||| ||||||||||| ||||| ||  | ||||| ||||| |
gtacgttcccatttcatcgaacctctccgagcgcgacgttaattgaaaaaaa--aggattactttgaggaacccttaatcggtaactgaatttgttttttttgtgtgttgtgctgtgttgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCTATGACCTCCATCAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G36610.2 (Glycine max), 3'ss of exon 1
------------aatgtaatcgcgagtaag--ttgataa-----attttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgt---agTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
             || | |||||   |     || | ||     |||              || | ||| || | ||    | || | |  ||   ||||| | || |||  |||||   |||||||||| || || ||||| || || |||||||| |||||| |||| || || || ||||| ||||||||||| ||||| ||  | ||||| ||||| |
gtgcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattt-tgaggaacccttaatcgat--atctgattttttttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G36610.3 (Glycine max), 3'ss of exon 1
----------aatgtaatcgcgagtaag--ttgataa-----attttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgt---agTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
           || | |||||   |     || | ||     |||              || | ||| || | ||    | || | |  ||   ||||| | || |||  |||||   |||||||||| || || ||||| || || |||||||| |||||| |||| || || || ||||| ||||||||||| ||||| ||  | ||||| ||||| |
gcgctctcattatttcatcgcacctctcccttcacaacgttgattgaaaagaaaaaagattcaattt-tgaggaacccttaatcgat--atctgattttttttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G36880.3 (Glycine max), 3'ss of exon 1
------------------aatgtaa-tcgcgagtaagttgataaattttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                  | || |  || |   | |     |  |||   |  |       ||   ||| || | ||    | || | | | |    | || | ||||   |  || |||||||||| || || ||||| || || |||||||| |||||| |||| || || || ||||| ||||||||||| ||||| ||  | ||||| ||||| |
gtgcgctcccattattttattgcacctctcccttcacaacgttgattgaacaataaaaggattctattt-tgaggaacccttaatcgataactgatttctttttttgtgtgtgttgcagTCTCTGGTGGCGAACGAGGATTTCCAGCACATTCTGCGTGTGCTGAACACCAACGTGGATGGGAAGCAGAAGATAATGTTCGCAATGACCTCCATCAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S242_94V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgtt---gttgattgtg--tagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                                           ||      | ||| | |||  | | ||   |||||||  |  |  |  ||| | | | ||   |||||  |  |  | ||  |    | || |||||   |||| ||  ||||    ||||| ||||| ||||||||||||||| |||| ||||| || |||||    |||||||| ||||||||||| || || || || |
gtgcgtgttcatcgcttcctccccatgcagctttcgtcgactcgtttctttgcgtacgatga-gattgttatttttttttcttccaaatgttgt-acacttcta--gggttcgtgcatctgtgactgaaagctggttgtgaacagTCGCTCATTGCGGGCGAGGAATTTCAGCACATTCTTCGTGTGCTGAACACTAACGTCGATGGACGTCAGAAGATCATGTTTGCCCTGACTTCGATTAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S14_433V6.1 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------------------------aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatg-----tgaaattactgat---------gggttaattgaattttg--------tgttgttgattgtg--tagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                                                           | |    | |  |   ||  |   ||||   |||||||| ||| |||| |      | |  ||| ||||         ||||||||||   | ||        || ||  | |||||   |||| ||| | ||   |||||||||||| |||||||||||||||||||| ||||| || |||||    || ||||||||||||||| | ||||| || || |
gtttgtgctcctctgctgttgcgtatatctgtggtgtcgttttttgtttggtactgagttctgggtgtgtttttttttttttttttttttttttttttttttggtttttcaatttttaggttaatgatcgtttgctagggttaattgggctgtgactgaggttggtggcggttgtggccagTCGCTGATCGCGGGTGAGGAGTTTCAGCACATTCTTCGTGTGTTGAACACTAACGTCGATGGACGTCAAAAGATTATGTTTGCCTTGACCTCCATTAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S215_71V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatgtgaa-attactgatgggttaattgaattttgtgttgttgattgtg-tagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                                                  || ||     ||  ||  |     |    |||| | | |   ||||| ||     | |||||   |||  |||   | ||||||   |||  ||  |||| ||  ||||    |||||||| || ||||||||||||||  ||||||| || || |||||    |||||||||||||||||||| ||||| ||||| |
gtgtgtctgatctgcctcgtccttgtcattgtgctgctcttcttggctcttattcagtgctatcttcgtgttcgtgaaattttatgtttagggtttacgtctttgtgactga-aagttggttg---tgtgtgtttccgatgttggcagTCGCTCATTGCGGGCGAGGAGTTCCAGCACATTCTTCGTGTTCTGAATACCAACGTCGATGGGCGTCAGAAGATTATGTTTGCCCTAACCTCCATCAAGG

upper sequence: AT4G09800.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S14_438V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------aatgtaatcgcgagtaagtt--gataaattttgcgttttttttgtttagttt--atgtgaaattactgatgggttaattgaattttgtgttgttgat-tgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                                ||  |    |    |  |||  | |   ||| | || ||||||| |    ||    |||       | |||   ||| |   ||  |  | || | | ||  ||||| ||  | ||   ||| ||||||||||| |||||||||||| ||||||| || || |||||   ||||||||| ||||| ||||| ||||| || ||||
gtgggtagtttctcccacctgtgctacacgtaaaaatttcagtttttcggttccgttctgtttggagtgttttttgctcgactttagggtgtgcaggttcatgatctaaattggttcagaatggtgggtgtgactagTCGCTCATCGCGGGTGAAGAGTTTCAACATATTCTTCGTGTGCTGAATACAAACGTCGATGGACGGCAGAAGATCATGTTCGCCCTGACCTCCATTAAAG

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|116431165|gb|EG473757.1|EG473757
EST:     AAACCTCATCTCTGCTAATCAAAATG                         TCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACT
genomic: AAACCTCATCTCTGCTAATCAAAATGgtaattaggg ... gattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACT
EST: gi|164204771|gb|EL973135.1|EL973135
EST:     GCTAATCAAAATG                         TCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACT
genomic: GCTAATCAAAATGgtaattaggg ... gattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACT
EST: gi|124723746|gb|EH815148.1|EH815148
EST:     CTAATCAAAATG                         TCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACT
genomic: CTAATCAAAATGgtaattaggg ... gattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG
                        ttaattgaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtaatcgcgagtaagttgataaattttgcgttttttttgtttagtttatgtgaaattactgatgggttaattgaattttgtgttgttgattgtgtagTCTCTGGTTGCAAATGAGGAGTTTCAACACATTCTTCGTGTGTTGAATACTAATGTTGATGGTAAGCAGAAGATTATGTTTGCCCTTACCTCTATCAAAG

- - - - - - - - - - - - - - - - - - - - tgtttag