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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaattaaatatttccatttgggaaagtctcatgtattcagtaataataactcagtctttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG

Basic information

species Arabidopsis thaliana
transcript AT1G30400.2
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA13G29180.1 (Glycine max), 3'ss of exon 24
------------------------gtacttaattaaatatttccatttggga-aagtctcat-gtattcagtaataataactcagtctttt--tggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG
                        ||   |  |    | |||   || | || |  | |  | | | |||||| | || | | |    | |  |   |||||| |||||||||| ||||| |||||||||||||| |||||  ||||||||||| | || || || || || ||||| |||||| | || ||||| ||||
ctattatggatatgctttagaagtgtgaattctcctgtgtttgttttagagatatatattgttgaagtcagtatttattaatgaaaagtgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGACAAAGACAACTGTTGAGTCTTTCTCGGGCTTTATTGCGTAGATCAAAGATATTAGTACTTGACGAAG

upper sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: GLYMA15G09900.1 (Glycine max), 3'ss of exon 24
-----------------------gtacttaattaaatatttccatttgggaaagtctcat----gtattcagtaataat-aactcagtctttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG
                       ||||  | |    | | |   |||   | |     ||    | |   |||| | || ||   |    |  |   |||||| |||||||||| ||||| ||||||||||| || || ||  ||||||||||| | || || || || || ||||| || ||| | || ||||| ||||
acgtattatggatatgcttagaagtacaaattgtcctttgtttgttttacagatatatattgttgaagctagtatttattaatgaaaatgtggtatccagGTATCTGAGGCAGGCGAGAACTTCAGTGTTGGGCAAAGGCAACTGTTGAGTCTTTCCCGGGCTTTATTGCGTAGATCGAAAATATTAGTACTTGACGAAG

upper sequence: AT1G30400.1 (Arabidopsis thaliana), 3'ss of exon 25
lower sequence: Vv10s0003g04390.t01 (Vitis vinifera), 3'ss of exon 24
-----------------gtacttaattaaatatttccatttggg-------aaagtctcatgtattcagtaataataactcagtctttt----tggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG
                  ||  |  | || | | |   ||||         | |||  ||  | || | ||  || || ||   | | |    ||   ||||  | ||||| |||||||||||||||||||||||||| ||  | || |||||||| || |||||| | || ||||| ||||| ||||||||||||||||
taggtaaatgggccctgatatgttgtcaattctgttgttttgaactaattcagagtaacaacttttaaatagaaacaattcttccatgtggtatgtgaagGTTTCCGAGGCCGGAGAGAATTTCAGTGTTGGACAGAGGCAACTTTTAAGTCTTGCTCGAGCATTGCTGCGGAGATCAAAGATTCTTGTTCTTGATGAAG

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|116481322|gb|EG523914.1|EG523914
EST:     CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAG                         GTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
genomic: CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAGgtacttaatt ... ttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
EST: gi|125241888|gb|EL255973.1|EL255973
EST:     TTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAG                         GTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
genomic: TTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAGgtacttaatt ... ttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
EST: gi|116442965|gb|EG485557.1|EG485557
EST:     CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAG                         GTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
genomic: CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAGgtacttaatt ... ttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
EST: gi|116442966|gb|EG485558.1|EG485558
EST:     CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAG                         GTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
genomic: CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAGgtacttaatt ... ttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
EST: gi|116481323|gb|EG523915.1|EG523915
EST:     CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAG                         GTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT
genomic: CACACTTGAAAGATACTATCCGCAGAAATCCTCTTGGTCTTGATGCTGAGgtacttaatt ... ttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatttgggaaagtctcatgtattcagtaataataactcagtctttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG
                               taataac  putative branch site (score: 1)
                                          tcttttt  putative PPT
                     tattcagtaataataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaattaaatatttccatttgggaaagtctcatgtattcagtaataataactcagtctttttggtcagGTAACTGAGGCAGGAGAGAATTTCAGTGTTGGACAGAGACAGTTGTTGAGTCTTGCACGTGCATTGTTACGAAGATCTAAGATACTTGTTCTTGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA