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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtggtgcgtactgtgaacaaaacagaatggattactaatcaactgtaagctcttaactgttgcttttcattctaacatgattcacttttgtaacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTACTTGGAGTCGAT

Basic information

species Oryza sativa
transcript LOC_Os02g07260.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G382914_T02 (Zea mays), 3'ss of exon 2
----gtggtgcgtactgtgaacaaaacagaatggattactaatcaactgtaagctcttaactgttgcttttcattctaacatgattcacttttgtaacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTACTTGGAGTCGAT
     | ||    |     | |      |  | || |    | ||||  |||  | ||  || ||  ||||  |  |||    |||   |  ||  |  | ||||| ||||| || ||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| || 
actaatagta-acaagtcaaccttttttgggttgagtgt--agcaacaataattttttgtctttta-tttttgtaataatgcaatttgttgatgccattttcagGGTCGTCCAAAAGGTGTCACCCCAAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTCCTTGGAGTTGAA

upper sequence: LOC_Os02g07260.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 1
gtggtgcgtactgtgaacaaaacagaatggattactaatcaactgtaagctcttaactgttgcttttcattctaac-atgattcacttttgtaacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTACTTGGAGTCGAT
||  |  ||    |     |      |||||||  |         ||   | |||  ||||    || ||   |   |||||||    ||||    | ||||| || || |||||||| || || |||||||||||||| |||||||| ||| |  ||||||| || |||||||| || 
gtttt-tgtttctttcctgactttctatggattcatttcttggaatatatttttacttgttctaatttatgaaactgatgattctgaattgtcgttttcagGGGCGCCCAAAGGGTGTTACACCTAAGTACAGCTTGAAACCTCTTGTGCCAAGGCTGTCTGAACTTCTTGGAGTTGAG
















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|33794558|gb|CF323166.1|CF323166
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|58675077|gb|CK063764.1|CK063764
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|88362801|gb|CI614157.1|CI614157
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTA-AGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|29656603|gb|CB652878.1|CB652878
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|14574908|gb|AU197198.1|AU197198
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAA-GGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|13806339|gb|AU181481.1|AU181481
EST:     GCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: GCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|33794797|gb|CF323278.1|CF323278
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|58667980|gb|CK056666.1|CK056666
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|33690674|gb|CF318913.1|CF318913
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|300216018|gb|HO088644.1|HO088644
EST:     GGCGCC-AGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: GGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|13904803|gb|BF889441.1|BF889441
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|2310338|gb|C26493.1|C26493
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGG-TGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|29676664|gb|CB672939.1|CB672939
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|33793275|gb|CF322518.1|CF322518
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|33797454|gb|CF324587.1|CF324587
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|29686925|gb|CB683200.1|CB683200
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|32947941|gb|BP184513.1|BP184513
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|29656155|gb|CB652430.1|CB652430
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|29614437|gb|CB619450.1|CB619450
EST:     TCGAGAAGGGCGCCACGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|27554028|gb|CA997928.1|CA997928
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|4878615|gb|AU062914.1|AU062914
EST:     CTCCTCGAGAAGGGCGCCAAGGTCATCCTCATCAGCCATCTG                         GGCCGTCCGAA-GGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: CTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
EST: gi|117247218|gb|CT848558.1|CT848558
EST:     TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTG                         GGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA
genomic: TCAAGTTCCTCCTCGAGAAGGGCGCCAAGGTCATCCTCGCCAGCCATCTGgtcagtgagc ... taacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagctcttaactgttgcttttcattctaacatgattcacttttgtaacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTACTTGGAGTCGAT
                                       cttttgt  CT-rich tract
                  ttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggtgcgtactgtgaacaaaacagaatggattactaatcaactgtaagctcttaactgttgcttttcattctaacatgattcacttttgtaacctccagGGCCGTCCGAAGGGTGTCACCCCCAAGTACAGCTTGAAGCCTCTTGTTCCACGCTTGTCTGAGCTACTTGGAGTCGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG