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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgatgattttttccccctcagagttgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG

Basic information

species Arabidopsis thaliana
transcript AT2G24200.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G36530.1 (Glycine max), 3'ss of exon 6
-------------gtatctgatgattttttccccctca---gagttgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG
             |     |||||||| ||       |   | || |  ||||  ||  ||||  ||   |    |   |       |     |  |||||| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||||||||| || || |||
ttattggagttttggcctcgatgatttatttaatagaacatgtgtagtactttacctcgtttttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAACCAAGGTGTTGAAAAG

upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G08150.1 (Glycine max), 3'ss of exon 6
-------------gtatctgatgattttttccccctca---gagttgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG
             |    ||||||||| ||     | |   | || |  ||||  |   || |  ||   |    |   |       |     |  |||||| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||| ||||| || || |||
taattggagttttggccttgatgatttatttaatataacatgtgtagtactttaccccgttcttgtactgaggatttgataggcttaacatcttccgtagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAG

upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G22730.1 (Glycine max), 3'ss of exon 6
--gtatctgatgattttttccccctca-gagttgagctttta--ctgtttttcctatgaaatgctaattgt---tggcgatggtgt--------gtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG
  |||  |    || | |        | || ||||  ||||   || ||    ||||  |||   |   ||   || |  |||| |        |||||||| || ||||||||||| || ||| | || || || ||||||||||| ||||||||||||||||| || |  || |||
aagtacgtttaaatctgtgaaagtctatgaattgaagttttgacctcttagatctatataatagcacaggtgtatgacattggtttaacctcttgtgtagGTTAATAACACAGATGCAGAGGGTAGGCTTACCCTGGCAGATGCTCTGGTGTATGCTTGTAACCAGGGTGCTGAAAAG

upper sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 6
-------------gtatctgatgattttttccccctca---gagttgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG
             |    ||||||||| ||     | |   | || |  ||||  |   || |  ||   |    |   |       |     |   ||||| |||||||| |||||||||||| | || || || ||||||||||| || ||||||||||| ||||| || || |||
taattggagttttggccttgatgatttatttaatataacatgtgtagtactttaccccgttcttgtactgaggatttgataggcttaacatcttccctagGTTAACAACACTGATGCTGAAGGTAGACTTACCCTGGCAGATGCTCTGGTATATGCTTGTAATCAAGGTGTTGAAAAG

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|116409488|gb|EG452080.1|EG452080
EST:     GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAG                         GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
genomic: GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAGgtatctgatg ... gtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
EST: gi|125254104|gb|EL268189.1|EL268189
EST:     AAGACCATTGAG                         GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
genomic: AAGACCATTGAGgtatctgatg ... gtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
EST: gi|116409481|gb|EG452073.1|EG452073
EST:     GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAG                         GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
genomic: GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAGgtatctgatg ... gtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
EST: gi|116409618|gb|EG452210.1|EG452210
EST:     GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAG                         GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
genomic: GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAGgtatctgatg ... gtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
EST: gi|116409637|gb|EG452229.1|EG452229
EST:     GAATGAGACCTGGAGACGTCATCACTGCCTCAAACGGAAAGACCATTGAG                         GTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG
genomic: GAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAGgtatctgatg ... gtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG
                           tgctaat  putative branch site (score: 2)
                    tatgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgatgattttttccccctcagagttgagcttttactgtttttcctatgaaatgctaattgttggcgatggtgtgtgtagGTCAACAACACAGATGCTGAAGGTCGTCTAACACTCGCAGATGCTCTAGTGTATGCTTGTAACCAAGGCGTCGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG