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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtatagtgtataccaaccctctgatcaccatcgaaattggttatatgtaaataatttggtgtgtgtaaatgcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCACTTGAGATGCTTAGGACAAGCATGAACCTAGAAGACACTCTCCACGAG

Basic information

species Arabidopsis thaliana
transcript AT2G47630.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G47630.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g21310.1 (Oryza sativa), 3'ss of exon 2
--gtctgtatagtgtataccaaccctctgatca--ccatcgaaattggttatatgtaaataatttggtgtgtgt----------------aaat---gcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCACTTGAGATGCTTAGGACAAGCATGAACCTAGAAGACACTCTCCACGAG
   |||| | | |  |||| |    ||  |        | |   |||   ||||  |   | ||||||||||                  ||||    ||| | ||||| |||||||||||||| || |||||||| |||||||| ||||||||||||||||| ||||| |||||| || |||| ||||   |   | ||
atttctgaacatttgatac-agtggtccaacagatttgttgtcgttgagcatataaactcagtttggtgtgttctttgccatgccatgccaaatttaacagATCAGGAAGAACAAGCTGATATACCAGGACAAGCCGAGGCTCAAGACCGCACTTGAGATGCTCAGGACCAGCATGTACGTAGAGGACAGCTTGTCCAAG
















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|86077460|gb|DR373217.1|DR373217
EST:     CTCGTCAAGCGAGAAGAG                         GTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCA
genomic: CTCGTCAAGCGAGAAGAGgtctgtatag ... gtaaatgcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCA
EST: gi|86040705|gb|DR336460.1|DR336460
EST:     AAAAGACGTGATTGACGCTGCTTTTCA-GGACCTCGTCAAGCGAGAAGAG                         GTAAGGAACAACAAGCTGATATATCAAGNNNNGCCTAGGCTCAAAACCGCA
genomic: AAAAGACGTGATTGACGCTGCTTT-CAAGGACCTCGTCAAGCGAGAAGAGgtctgtatag ... gtaaatgcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCA
EST: gi|164039562|gb|EL989447.1|EL989447
EST:     GACGCTGCTTTCAAGGACCTCGTCAAGCGAGAAGAG                         GTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCA
genomic: GACGCTGCTTTCAAGGACCTCGTCAAGCGAGAAGAGgtctgtatag ... gtaaatgcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCA
EST: gi|125004637|gb|EL076906.1|EL076906
EST:     CAAAAGACGTGATTGACGCTGCTTTCAAGGACCTCGTCAAGCGAGAAGAG                         GTAAGGAACAACAAGACTGATATATCAAGACAAGCCTAGG
genomic: CAAAAGACGTGATTGACGCTGCTTTCAAGGACCTCGTCAAGCGAGAAGAGgtctgtatag ... gtaaatgcagGTAAGGAACAACAAG-CTGATATATCAAGACAAGCCTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatcaccatcgaaattggttatatgtaaataatttggtgtgtgtaaatgcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCACTTGAGATGCTTAGGACAAGCATGAACCTAGAAGACACTCTCCACGAG
 ctctgat  putative branch site (score: 4)
              aaattggttatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtatagtgtataccaaccctctgatcaccatcgaaattggttatatgtaaataatttggtgtgtgtaaatgcagGTAAGGAACAACAAGCTGATATATCAAGACAAGCCTAGGCTCAAAACCGCACTTGAGATGCTTAGGACAAGCATGAACCTAGAAGACACTCTCCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG