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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgaaaaaaaaagattggtggtctagggccattgcttttattatttctgtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC

Basic information

species Arabidopsis thaliana
transcript AT4G01770.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G01770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G09360.1 (Glycine max), 3'ss of exon 1
-ttgaaaaaaaaag-attggtggtctagggccattgcttttattatttct-gtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
 |||         |  ||| |  | | |  |  |  |||   || ||||| |||||||  |   | || |    ||  |   ||  | ||   | | | ||||||||||||||| || |||||  |  ||||    |||||  || | ||||||||||| || || | ||| |||||||| ||||||||||||||||||||| 
cttgtctgccgtggtgttgattat-tggaactgtctcttaatttctttctcgtgtgtggtgctgagttttaaaatccatt-cttgtttatttca-ctgtctagGGTTTCTTCAACTTTACAGCAAGGCGGCCAAGCCATCTGCTGAAGATTTTGGAGCTTGGATATAGTGTGATGTACAATGATGTTGATATGGTTTGGTTGG

upper sequence: AT4G01770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv15s0046g01630.t01 (Vitis vinifera), 3'ss of exon 1
--ttgaaaaaaaaagat--tggtggtctagggccattgct--tttattatttctgtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
  ||| |      |  |  |  | ||| |  |  ||   |  |||||    | | ||| |   ||  | |||   | |   | ||| | |  ||||    |   |||| ||||||||||| ||  | |||||||| |  |||||  || | ||||||||||| || || |||||||||||||| |||||||||||||| |||||| 
ctttgcatttcctatttcttctttgtcgatagtgatgaatattttatagagtttttgtattg-gattatttaaaatgtttttgattgatt--tcat---tgtacagGGGTTCTTCAATTTTACTTCCCGAAGGCCTCGCCATCTGCTGAATATTTTGGAGCTTGGATATAATGTTATGTACAATGATGTTGATATGGTGTGGTTGG

upper sequence: AT4G01770.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0019g04760.t01 (Vitis vinifera), 3'ss of exon 1
ttgaaaaaaaaagattggtggtctagggccattgcttttattatttctgtgtgtgaagaaaacttatgttttca--ctaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
    | | |     ||  |  | |       |||||  ||||  |      |         | |  | |||  |   | |||   | ||   ||   || |||||||||| ||||| ||  |||||||||| |  || ||  || | ||||||||||| || |||||||||||||| || |||||||| ||||| |||||| 
-gctatacactgtctttctcattttcatttcttgctgatattgatcaatcatcaatgtgggattagtttttgaagtttgattgcttgatttcattatac-agGGTTTCTTTAATTTTACTTCTCGAAGGCCTCGCCACCTACTGTACATTTTGGAGCTTGGATACAATGTTATGTATAATGATGTTGACATGGTATGGTTGG

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|116377474|gb|EG420066.1|EG420066
EST:     TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAG                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCT
genomic: TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCT
EST: gi|116384376|gb|EG426968.1|EG426968
EST:     TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAG                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
genomic: TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
EST: gi|116377409|gb|EG420001.1|EG420001
EST:     TCGATTCTAAAACCGCATTCAGTTTCGGTTCCCCT                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
genomic: TCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
EST: gi|116377428|gb|EG420020.1|EG420020
EST:     GCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCCT                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
genomic: GCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
EST: gi|116384206|gb|EG426798.1|EG426798
EST:     TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAG                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
genomic: TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
EST: gi|116378074|gb|EG420666.1|EG420666
EST:     TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAG                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
genomic: TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
EST: gi|116377453|gb|EG420045.1|EG420045
EST:     TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAG                         GGTTTCTTCAATTTCACAGCTCGAAGGCCTCAACATCT
genomic: TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCT
EST: gi|116377437|gb|EG420029.1|EG420029
EST:     TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAG                         GGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG
genomic: TTATTCCTCCAGCGCTCGATTCTAAAACCGCATTCAGTTTCGGTTCCCAGgtaaagtttt ... atccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC
                           cactaat  putative branch site (score: 2)
             aaaacttatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgaaaaaaaaagattggtggtctagggccattgcttttattatttctgtgtgtgaagaaaacttatgttttcactaatttactcatcatatccgactagGGTTTCTTCAATTTCACAGCTCGAAGGCCGCAACATCTCTTGCAAATTTTGGAGCTAGGTTACAATGTTATGTACAACGATGTTGATATGGTTTGGTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcatca