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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA

Basic information

species Arabidopsis thaliana
transcript AT2G33210.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G126878_T01 (Zea mays), 3'ss of exon 1
------------------gtgagttgaattttatccctaaatgtcaaattattttgc-ttattcc--ttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                  | |  ||    ||  | |||   | |     | || ||| || |||   || |  | |         | |  | ||  |  |||||||||| ||| | | ||||||||| |||||||| |||||||||||  ||||||| || |||||||| ||||||||||| || ||| | ||||||||  
tgaggtctactgataagtgcgcattttgattgtttccttgtttttgctcttttctgcattgttctgtttcaacttattggctgatttaaatgttc-tgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACACATG

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G416120_T01 (Zea mays), 3'ss of exon 5
------------------gtgagttgaattttatccctaaatgtcaaattattttgc-ttattcc--ttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                  |    ||    ||  | |||   | |     | || ||| || |||   || |  | |         | |  | ||  |  |||||||||| ||| | | ||||||||| |||||||| |||||||||||  ||||||| || |||||||| ||||||||||| || ||| | ||| | || |
tgtggtctactgataagtgcacattttgattgtttccttgtttttgctcttttctgcattgttctgtttcaacttattggctgatttaaatgttc-tgtagGATGGCAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTTGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAGCCCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 5
----------gtgagttgaatttta----tccctaaat--gtcaaattattttgcttattccttaaggtgaccaatgttatcatctct----tgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
          ||  | | |||| |     | ||    |   |||||||  | |  || | | ||  | ||    |  |||     |      |  || |||| || || ||| | | ||||||||| |||||||| |||||||||||  | ||||| || |||||||| ||||||||||| || ||| | ||||| || |
ttatggtgctgtatgcttaattcttgtctttcccggcttcatcaaattgctctttttctgcattgtgctgtttcagtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G33910.1 (Glycine max), 3'ss of exon 6
-----------------------------gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                              ||  ||||||| |  || |  || |    ||  | ||  ||| | ||| ||   | ||  ||   ||    || |||||||||||||||| ||||  |||||| ||||||| ||||| || |||||| | |||||||||||||| || || || |||||||| |||| ||| |  || |
catcctcgttgcctcctccaaaggggtccatggtttgaattatg-ccatgcatttt---ttgatatggatatgc-ttagggc--ctaacatt--tataaactgtttcagGATGGCAAGACATTGTACAATGAGTTGGAAGTCGTTGAAGGAATGAAGCTCGACAGGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 6
------------------------gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                         ||| |  || ||  |   | ||| |  |   ||| |  ||  |  || |   | ||    ||||     ||   ||||||||||||| ||||| | ||||||| ||||||||||||| || |||||| | |||||||| ||||| || || || ||||| || ||    || |  || |
tcatttcttctcctgccattatccctgattccaacttagtt--tgaatttttacccattgtattttgtattttacaaggcctg-attattggaact-atttcagGATGGCAAAACCTTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAATGATAAGAACCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 6
gtgagttgaattttatccctaaatg-----------tcaaattattttgcttattccttaaggtga-----ccaatg-----ttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
 | |      ||   |||   || |           |  ||||||   |   |||  | ||  |||     | |  |      | | ||    || |||||||||| ||||| ||||  |||||| |||||||||| || || |||||| | |||||||||||||| || || || |||||||| |||| ||| |  || |
-tcatcctcgttgcctcctccaaaggggtccgtggtttgaattatgccgtgcatttatcaatatgaatatgctagggcctaacttttataaactgtttcagGATGGTAAGACATTGTACAATGAGTTGGAAGTTGTGGAAGGAATGAAGCTCGACAGGGGATACATTTCTCCATATTTCATAACAAACCAGAAGAACCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 6
-----------------------gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                          | ||  |  |||    ||| | |       | |    | |  ||||  ||| |  ||  |   | |  ||   |||||||||||| || || | ||||||| ||||||||||||| || |||||| | |||||||| ||||| || || || ||||| || |||   || |  || |
tcatttctttttctgccattatccctaattccaacttagttttaattttttccccttgtattctgtatcttacagtgcctgatcattgtaaccatt---tcagGATGGCAAAACATTATATAATGAGTTGGAAGTTGTTGAAGGAATGAAGCTCGACAGGGGCTACATATCTCCTTATTTCATTACAAACGATAAGAACCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtgagttgaat-tttatccctaaat---gtcaaattattttgcttattccttaagg-tgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                | | || ||| ||||| | || ||   |   |||| |||   ||   |  || |  | ||   |   ||      ||| | |||||||| ||||| |||| ||||||  |||||||||||||||| |||||| | || || || ||||| ||||| || || ||||| |||| |||||| ||||
ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactctttccatggggaattgttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 6
-----gtgagttg--aattttatccctaaatgtcaaattattttgcttattccttaaggtgacc-aatgttatcat------------ctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
      | || |   |||||   |  || | | |  |  || |     ||   | || |  ||| | || |  | |            |  |   | ||||| || || ||  ||||||||||| |||| ||||| |||||||||||| | ||||| ||||| ||||| || || ||||| || ||  | || || ||||
ttgaaataagataccaatttgtgcattatacgcctcaggatatgatagataagtgaatgcaacctagtgctcccgtgatggacggttacgttccttgcagGACGGAAAAACTCTGTTTAATGAGTTGGAGGTTGTGGAGGGTATGAAGCTCGACAGAGGATATATCTCTCCCTATTTCATCACCAATTCTAAGACTCAAA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 6
-----gtgagttgaattttatccctaaatgtcaaatt------attttgctta--ttccttaaggtgacc----aatgttatcatctc---ttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
       |   |  ||| || |  ||  || || |        |||| | |||  | || |    ||  |     ||||| |||| |    ||    |||||||| ||||| || ||||||||| |||| ||||| ||||| |||||| ||||||||||||| || ||||| || ||||| |||||  | || || || |
cccacaaggtctccattctagcattatgtgccagagggtatagatttcgattaaatgccatctaatggtccagtgatgttctcatgtggtattatcacagGATGGAAAGACTTTATTTAATGAGTTGGAGGTTGTGGAGGGCATGAAGCTTGACAGGGGATATATTTCCCCCTATTTCATCACTAATGCAAAGACCCAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S52_245V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------------------------------------------------------------------------------------gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaa-ggtgaccaatgttat-catctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                                                                                                               | || | | | |       | |||        ||||| |  ||||  | |  |||||          |  |  ||  |  ||||||| || || ||||| |||||  |||| |||||||||||||||||| | ||||| ||||| || ||||| |||||||| || ||  |||| ||||| |
gtaagtagatgtctgtgtgtcatactctcttgttttaccattgcggatttagttatggtttgcttcccgtgataggtacaagacgatgctgttgatgtcaatttttgacccgcgattgggagtagcgtatttaatagtgg--catttttccaattcaatgatagtgactgggaaggggcggcgttttctgtagGATGGAAAAACTTTGTTCAATGAATTGGAGGTTGTTGAGGGTATGAAGCTCGACAGAGGATATATTTCCCCTTACTTCATTACCAATGCGAAGACACAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgatt--cagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                           ||  |   |   ||||   ||     ||| ||  || | ||      |    ||||||||||||||||||   || ||||| || ||||| |||||||||||  | |||||||||||||| ||||| || ||||| |  ||| | || ||||| |
-------------------------gtaagctgggtcatttatggtttttatcgacaaac-ttctgatgagagaaacaacagGATGGCAAGACCTTGCACAACGAGCTAGAGGTTGTGGAGGGTATGAAATTGGACAGGGGATACATTTCCCCCTATTTCATTAACAACGCTAAGACACAGA

upper sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32351 (Selaginella moellendorffii), 3'ss of exon 4
gtgagttgaattttatccctaaatgtcaaattattttgcttattccttaaggtgaccaatgt-tatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                           ||  |   |   ||||   ||     ||| ||  | |  |           ||||||||||||||||||   || ||||| || ||||| |||||||||||| | |||||||||||||| ||||| || ||||| |  ||| | || ||||| |
-------------------------gtaagctgggtcatttatggtttttatcgacaaacttctgacgagagaaacaacagGATGGCAAGACCTTGCACAACGAGCTAGAGGTTGTGGAGGGTATGAAGTTGGACAGGGGATACATTTCCCCCTATTTCATTAACAACGCTAAGACACAGA

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|47829841|gb|CK119525.1|CK119525
EST:     TTGCAAAGGCTATGGAAACTGTCGGCAAAGAGGGAGTGATCACAATTCAA                         GATGGCAAGACCTTGTTTAATGAG
genomic: TTGCAAAGGCTATGGAAACTGTCGGCAAAGAGGGAGTGATCACAATTCAAgtgagttgaa ... cttgattcagGATGGCAAGACCTTGTTTAATGAG
EST: gi|116483327|gb|EG525919.1|EG525919
EST:     TTGCAAAGGCTATGGAAACTGTCGGCAAAGAGGGAGTGATCACAATTCAA                         GATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATT
genomic: TTGCAAAGGCTATGGAAACTGTCGGCAAAGAGGGAGTGATCACAATTCAAgtgagttgaa ... cttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaattattttgcttattccttaaggtgaccaatgttatcatctcttgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA
                                            tcttgat  putative branch site (score: 4)
                                       tcatctctt  CT-rich tract
     ttattttgcttatt  TA-rich tract