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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgatgagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG

Basic information

species Arabidopsis thaliana
transcript AT3G52220.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA02G12330.1 (Glycine max), 3'ss of exon 1
--agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgatgagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG
  | |   ||  ||   |  |||    |||   | |   || ||  | |  |    ||| |  ||  |  ||   |  |||  |||   | |  |||  ||||||||| |||||| || || || ||||||||  |||||||||||||| | |||||||||||||| || ||||||||||||||||| ||||
tcacaaacttcatgcttaggagtaaaaaaactcatg-catataattttaattatctatg-tatgatattgatgtttgtttgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGCTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCTGTTGGAAGATGGCAGAAAG

upper sequence: AT3G52220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G06270.1 (Glycine max), 3'ss of exon 1
agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgat--gagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG
 |||  ||      | | |   ||   |  ||| |  |     ||        ||||||    | |   |||   | |  |  |||   | |  |||  ||||||||| |||||| || || || | ||||||  |||||||||||||| | |||||||||||||| || || |||||||||||||| ||||
-gatt-ttcacaaaattcatgcttaggagtaaaaaacttttgtatataacttcaatgatttatgtatgatatcgatgaacgtgttttactcttgatggccagAATTCACTTGGGAGGATGTGAAAGTTGATAAGCATAGGGAGAACTATCTTGGTCACAGTATCAAGGCTCCGGTTGGAAGATGGCAGAAAG

upper sequence: AT3G52220.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0101g00090.t01 (Vitis vinifera), 3'ss of exon 1
agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgat-----gagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG
      || ||     |  || ||   |||||    |   ||    |  ||   |  |      ||  | |  | | ||  |     || | |   ||||| ||||||| |  |||||||| ||||||| ||||||| |  | ||||||||| | |||||||||||||| |||||||||||||||||||||||||
-----tttcttctttctctgtcttactatcaatagggcctaagcctatttgtagacaactcatggatgattgaacttcttgtaattattttcttgtaatgtccagAATTTAAGTGGGATGATGTCAAGGTTGATAAACACCGAGAGAACTATCTTGGTCACAGTATCAAGGCCCCTGTTGGAAGATGGCAAAAAG

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|163969165|gb|ES116043.1|ES116043
EST:     TCCAAC-AGGGGAGGTGTTCGCGGTGGTCGAGATC                         AATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGG
genomic: TCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATCgtaagtttca ... aaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGG
EST: gi|301503170|gb|HO208710.1|HO208710
EST:     GTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGTGTGGTCGAGATC                         AATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGG
genomic: GTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCG-GTGGTCGAGATCgtaagtttca ... aaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGG
EST: gi|164105763|gb|ES133372.1|ES133372
EST:     GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATC                         AATTCAGTTGGG
genomic: GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATCgtaagtttca ... aaatgtgcagAATTCAGTTGGG
EST: gi|125113267|gb|EL164142.1|EL164142
EST:     GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATC                         AATTCAGTTGGGA
genomic: GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATCgtaagtttca ... aaatgtgcagAATTCAGTTGGGA
EST: gi|301502507|gb|HO208047.1|HO208047
EST:     GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATC                         AATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGG
genomic: GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATCgtaagtttca ... aaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGG
EST: gi|164029774|gb|ES192432.1|ES192432
EST:     GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATC                         AATTCAGTTGGGA
genomic: GGTTTCGATGTATCATCCAACGAGGGGAGGTGTTCGCGGTGGTCGAGATCgtaagtttca ... aaatgtgcagAATTCAGTTGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagctgctaatgatgagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG
                         tactaat  putative branch site (score: 1)
                    tctattactaattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatcgtttttggcaattagttttcaaatcaaagatgtagaacatgagctgctaatgatgagaactctattactaattgaatttgtttataaatgtgcagAATTCAGTTGGGATGAAGTCAAGGCTGATAAATATAGGGAGAACTATTTGGGTCACAGTATCAAAGCCCCTGTTGGAAGATGGCAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - -gtttttg
- - - - - - - - - - - - - aatcaaa
- - - - - - - - - - - - - - - - - - - - aacatga
- - - - - - - - - - - - - - - - - - - - - - - - ctgctaa