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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaacaattttaatactacacagattccctttggccttgtttagacttgtggtttgaagtttgtgctgttttcttttggtaacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGGATATCATTGGCCGGATTATCTCTGGCCAAATGCGAGTATCTTGCTGATG

Basic information

species Arabidopsis thaliana
transcript AT4G31990.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 10
---------------------------------------------gtatgccaacaattttaatactacaca----gattccctttggccttgtttagacttgtggtttgaagtttgtgctgttttcttttggtaacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGGATATCATTGGCCGGATTATCTCTGGCCAAATGCGAGTATCTTGCTGATG
                                              |   |     ||||    | || | |    || | |           || | ||       |     ||  |  | |  |   || |||    |||||| ||||| ||||| |||||||||||  | || ||||| || || ||||| || || ||||| ||||| || ||||| ||||||||||| || ||||| |
gtgacatatgctttaaattttcacagataacacttccattcttctatcgactggtgatttctcca-tatataatgtgactgcaaacactgcaattcacacaatacactaagtattcttaatttgattcgtttgtattt-gcagAGTGATAATATGACCGACAAATGGCACATATACATGACAAAGGATGGGAGAATTTCGTTGGCTGGATTGTCCCTGGCTAAATGCGAGTACCTAGCTGACG

upper sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 12
--gtatgccaacaatt--ttaatactacacagattccctttggccttgtttagacttgtggtttgaagtt-tgtgctg--ttttcttttggtaacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGGATATCATTGGCCGGATTATCTCTGGCCAAATGCGAGTATCTTGCTGATG
  |  | | ||||| |   |     |     |  |   | |       | |     |||    || | || |    ||  |||||| || ||  | | ||||| || || |||||  | || ||||||||||| ||||| || ||||||||||| |||||||| ||||| ||| ||||||||||||| |||||||| ||||
tagcttcctaacaagtgactgtagttttggtggctgtttatactagcatatcattctgtttcctggacttatactttggcttttctctttgtc-caatcagAGTGAGAATATGACAAATAAGTGGCATGTGTACATGACCAAGGACGGGAGGATCTCATTGGCTGGATTGTCTTTGGCCAAATGCGAATATCTTGCAGATG
















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|86079391|gb|DR375148.1|DR375148
EST:     TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAG                         AGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGG
genomic: TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaac ... taacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGG
EST: gi|164096396|gb|ES202371.1|ES202371
EST:     TGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAG                         AGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGG
genomic: TGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaac ... taacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGG
EST: gi|125295879|gb|EL309964.1|EL309964
EST:     TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAG                         AGCGATAACATGACGGACAAATG
genomic: TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaac ... taacgagcagAGCGATAACATGACGGACAAATG
EST: gi|125042553|gb|EL114822.1|EL114822
EST:     TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAG                         AGCGATAACATGACGGACAAATGGCATGT
genomic: TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaac ... taacgagcagAGCGATAACATGACGGACAAATGGCATGT
EST: gi|86083205|gb|DR378964.1|DR378964
EST:     TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAATCTCAG                         AGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGG
genomic: TTCTGAAGCAAATTGGCATGTTCTCTTTCACCGGCCTAAACAAAGCTCAGgtatgccaac ... taacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttgtttagacttgtggtttgaagtttgtgctgttttcttttggtaacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGGATATCATTGGCCGGATTATCTCTGGCCAAATGCGAGTATCTTGCTGATG
                                          tggtaac  putative branch site (score: 2)
                                  ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaacaattttaatactacacagattccctttggccttgtttagacttgtggtttgaagtttgtgctgttttcttttggtaacgagcagAGCGATAACATGACGGACAAATGGCATGTGTATATGACTAAAGACGGGAGGATATCATTGGCCGGATTATCTCTGGCCAAATGCGAGTATCTTGCTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT