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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttcacaatccatcatcacttcacttttgttctctctgaagattgcatttagctaactgtggagaacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG

Basic information

species Arabidopsis thaliana
transcript AT3G23990.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 16
--------gtgagtttcacaatc---catcatcacttcacttttgttctctctgaagattgc-atttagctaactgtggagaac--aaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
        |    ||||   ||     ||| | |  || | |   |    |||| || |||    | | |    || |    ||   |  |||||||||||||||| |||||||| ||||| ||||| ||||| || ||||||||||| || || ||||| |||||||| ||
gtatgattgaacctttcctcattgaatatcgtaatatcccatgattgtcgtctgtagtttgttgctgatccgtgtgcgatataccttatgtagGTGAATATGTGGACATGGTGAAGGCTGGTATCATTGACCCACTAAAAGTGATCAGAACTGCCTTGGTGGATGCTGCAAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G25630.1 (Glycine max), 3'ss of exon 16
-----------------------------gtgagtttcacaatccatcatcacttcacttttgttctctctgaagattgcatttagctaactgtggagaaca-aactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
                             ||    ||  || |||||           |  || |    ||||   ||      |  |   | |      || || ||||||||||||| |||||||| ||||||||||||||||||||| |||| ||||| |||||||| ||||||||||| || ||
gtgcgtgatttttgttttctttttccctagttgtgttttcattccatgtcagaagagatactgattctgctgacattttttgcaatttttttttctgcttcacaattagGTGAATATGTTGATATGGTTAAAGCTGGAATCATAGACCCTTTGAAGGTGATTAGGACAGCCTTGGTTGATGCAGCCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA20G19980.1 (Glycine max), 3'ss of exon 16
-------gtgagtttcacaatccatcatcacttcacttttgttc--tctctgaagat-tgc--atttagctaac----tgtggagaacaa-----------actagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
        | | | | |   | |  | | | |    |||  |||  | || |||||  | |  |||   || ||    | || | |               || |||||||||||| |||||||| ||||||||||||||||||||  |||| ||||| |||||||| ||||||||||| || ||
gtcggtgataattgttatctttctccctaattgtgttttcattccatgtcagaagagatactgattctactgacattttttgcaaatttttttcctgcttcacaagGTGAATATGTTGATATGGTTAAAGCTGGAATCATAGACCCCTTGAAGGTGATTAGGACAGCCTTGGTTGATGCAGCCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 16
-----------------------------------gtgagtttcacaatccatcatcacttcacttttgttctctctgaagattgcatttagctaactgtggagaacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
                                        | ||| ||   ||   || |||| | || ||   ||||     |||   | | |  |  ||      || | |||||||||||| |||||||| |||||||||||||| || ||  |||| || || ||||| || ||||||||||| || ||
gtaagggttcttggttgctttttgcggatgtgcttacttctgtcaaaagatatagccatttcattgttattgattctg----ctgccaattgttttccctgctttgtaatc-agGTGAATATGTTGATATGGTTAAAGCTGGAATCATTGATCCATTGAAGGTTATTAGGACCGCCTTGGTTGATGCAGCCAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 16
-------------------------------------------gtgagtttcac-aatccatcatcacttcacttttgttctctctga---agattgcatttagctaactgtggagaacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
                                           ||   |||||| ||       |    | | | || || | |   |   | | ||  |||   || |  | |   ||    ||||||||||||| |||||||| ||||||||||| || || || |||||||| || || |||||||||||||||||||| ||
gtttgtgctacatttgaattattttcgtttttatatgcccttagtttctttcaccaagtgggtgtggtattattattatttttttgcactcaaaatggttttgtttatccattgctcac---ttagGTGAATATGTTGATATGGTCAAAGCTGGAATTATTGATCCACTGAAAGTAATTAGAACAGCTTTGGTTGATGCTGCAAG

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: PP1S44_339V6.1 (Physcomitrella patens), 3'ss of exon 15
---------gtgagtttcacaatc---catcatcacttcacttttgttctctctgaagattgc-atttagctaactgtggagaacaaa--------ctagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
           ||  ||||   |     | |||||   ||  | ||   | ||  | || ||  || | | | |   |  |   ||          | ||| || || ||||||||||||||||||||||| || |||||| ||||||| ||||| || || || || ||||| || ||
aatttcatgcagaccttcatgcttgcgtaccatcagaccatctctgacttgtcaaatgagtgttatcttgttgatgttttaatgcatcatgtctccccagGAGAGTACGTGGATATGGTGAAAGCTGGAATTATTGACCCTGTGAAAGTAATCAGAACCGCATTCGTCGATGCAGCAAG

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|124737736|gb|EH829138.1|EH829138
EST:     ACCCAGACCTCGGTTATGATGCTGCTAAAG                         GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGA
genomic: ACCCAGACCTCGGTTATGATGCTGCTAAAGgtgagtttca ... aacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGA
EST: gi|47827837|gb|CK117521.1|CK117521
EST:     CAAGCTCTTGGAGCAAGATAACCCAGACCTCGGTTATGATGCTGCTAAAG                         GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGA
genomic: CAAGCTCTTGGAGCAAGATAACCCAGACCTCGGTTATGATGCTGCTAAAGgtgagtttca ... aacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGA
EST: gi|164003471|gb|ES090530.1|ES090530
EST:     GACCTCGGTTATGATGCTGCTAAAG                         GTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGA
genomic: GACCTCGGTTATGATGCTGCTAAAGgtgagtttca ... aacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacttttgttctctctgaagattgcatttagctaactgtggagaacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG
                               agctaac  putative branch site (score: 2)
     ttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttcacaatccatcatcacttcacttttgttctctctgaagattgcatttagctaactgtggagaacaaactagGTGAATATGTGGATATGGTGAAAGCTGGAATCATAGACCCTCTGAAAGTGATCAGGACAGCTTTGGTTGATGCTGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC