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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatgaatatgaatccgtactactaacaatttcaaacttttaaatgagctagttcaggcatgaattttgaaatctgatgtatacctttttttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACATCACACCGTCAGCCCTGGACCGGTGGGAGAAGAGGCTTGATGATCTCTT

Basic information

species Oryza sativa
transcript LOC_Os06g51290.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G300348_T04 (Zea mays), 3'ss of exon 2
aaatgaatatgaatccgtactactaacaatttcaaacttttaaatgagctagttcaggcatgaattttgaaatctgatgtatacct--ttttttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACATCACACCGTCAGCCCTGGACCGGTGGGAGAAGAGGCTTGATGATCTCTT
   |  |  | || |    ||  ||  ||| | || ||     ||  || | || |  |    | ||  |     | | | |  |   | || ||| ||||||||||||||||||||||||||||||||||||||| ||||| |||    |||| |||||  ||||  ||||||||||||||||||| ||||| ||||| ||
ctttatagttcaaactaccct-ttaggaatatgaatctcaagtattggcaattttaaacgaacacttc-aggcacggtatctgacgggtattgtttctgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGGCCAAACGCCAACTACATTACACCAACAGCTTTGGACCGGTGGGAGAAGAGACTTGAGGATCTGTT

upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 3
aaatgaatatgaatccgtactactaacaatttcaa-acttttaaatgagctagttcaggcatgaattttgaaatctgatgtatacctttttttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACATCACACCGTCAGCCCTGGACCGGTGGGAGAAGAGGCTTGATGATCTCTT
 |||   | | |||  | || |   |||| ||||| |||   | |    | ||   |   ||    | |    | |  | |    || | |   |   ||||||||||| |||| |||||||||||||| ||||| || ||||| || ||||| || ||  ||||| ||||  ||||||||   ||| | || ||||| ||
gaattt-tgtaaatatgcacaatacacaagttcaatactgaaacaaagacgagaggatttatattctcttttgtttcttatgattctctctccatgaacagTGTGGTGTCGGAGAACAGATGAGCTTGTTGATGGGCCTAATGCATCACACATAACCCCAACAGCCTTGGATAGGTGGGAGTCAAGGTTGGAAGATCTTTT
















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|29617545|gb|CB622557.1|CB622557
EST:     AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
genomic: AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATGgtacttcaac ... ttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
EST: gi|29682683|gb|CB678958.1|CB678958
EST:     AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
genomic: AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATGgtacttcaac ... ttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
EST: gi|157651867|gb|EX451501.1|EX451501
EST:     AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
genomic: AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATGgtacttcaac ... ttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
EST: gi|29617650|gb|CB622662.1|CB622662
EST:     AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
genomic: AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATGgtacttcaac ... ttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
EST: gi|58612838|gb|CK040550.1|CK040550
EST:     AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATG                         TGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA
genomic: AACTATGCTCATGACGGAGGACCGACGGCGCGCCATATGGGCCATCTATGgtacttcaac ... ttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagctagttcaggcatgaattttgaaatctgatgtatacctttttttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACATCACACCGTCAGCCCTGGACCGGTGGGAGAAGAGGCTTGATGATCTCTT
                          atctgat  putative branch site (score: 4)
                                  tatacctttttttttt  CT-rich tract
                                  tatacctttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatgaatatgaatccgtactactaacaatttcaaacttttaaatgagctagttcaggcatgaattttgaaatctgatgtatacctttttttttttgcagTGTGGTGTAGGAGGACAGATGAGCTTGTAGATGGACCAAATGCCTCGCACATCACACCGTCAGCCCTGGACCGGTGGGAGAAGAGGCTTGATGATCTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - -tgaatcc
- - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatgt