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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcacccgagtgttcgacgcgtgctcgtgacatgcgtggcgagctggtgtgtgagcgacattcgtcttgtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACGGCGAGCCGCAGCGAAGCGAACAGCGACCTGCCGGGGCCGGGGAGCAACC

Basic information

species Oryza sativa
transcript LOC_Os02g14440.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14440.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G117706_T01 (Zea mays), 3'ss of exon 2
gtacgttcacccga-gtgttcg-acgcgtgctcgtgacatg----cgtggcgagctggtgtgtgagcgacattcgtcttgtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACGGCGAGCCGCAGCGAAGCGAACAGCGACCTGCCGGGGCCGGGGAGCAACC
||| || ||  ||    || || |||        |||   |    | |  | |  |  ||      |||  | ||  |  ||  | |||||||| || || ||||||||||||||||| |||||| |||||||||| ||||||||||    |   || |||||||||||||||  |||||    |  ||
gtaagtacatacgttacgtacgtacgtagatagatgaaccgactccatcactacttactgctgctccga--tccgcatcatcggt-cagCTCGGAGGACCAAGCTGGGCGGTGCCGCTGGGCCGGCGCGACTCGACCACGGCGAGCCTGGCCCTGGCCAACAGCGACCTGCCGTCGCCGGTCTCCGGCC
















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|29657997|gb|CB654272.1|CB654272
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTG                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
EST: gi|29668843|gb|CB665118.1|CB665118
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCGG                         N
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcag-
EST: gi|29668843|gb|CB665118.1|CB665118
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCGG                         N
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcag-
EST: gi|29667713|gb|CB663988.1|CB663988
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTG                         CTCGGCGGGCCGAGCTGGGC
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGC
EST: gi|29656203|gb|CB652478.1|CB652478
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTG                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
EST: gi|29659429|gb|CB655704.1|CB655704
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTN                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
EST: gi|29660893|gb|CB657168.1|CB657168
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCC-TG                         G
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcag-
EST: gi|29660893|gb|CB657168.1|CB657168
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCC-TG                         G
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcag-
EST: gi|29659605|gb|CB655880.1|CB655880
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTG                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
EST: gi|29657998|gb|CB654273.1|CB654273
EST:     CGCCGACATNGTCGCCCTCGCCGCGCGCGACAGCACCGCCTTG                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGTCCGGTGCGACTCGACGACG
genomic: CGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
EST: gi|29655928|gb|CB652203.1|CB652203
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCGG                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
EST: gi|29663080|gb|CB659355.1|CB659355
EST:     TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTG                         CTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG
genomic: TCTCCTGCGCCGACATCGTCGCCCTCGCCGCGCGCGACAGCACCGCCCTGgtacgttcac ... gtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcgtgacatgcgtggcgagctggtgtgtgagcgacattcgtcttgtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACGGCGAGCCGCAGCGAAGCGAACAGCGACCTGCCGGGGCCGGGGAGCAACC
                                         tcttgtcc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttcacccgagtgttcgacgcgtgctcgtgacatgcgtggcgagctggtgtgtgagcgacattcgtcttgtccatgcagCTCGGCGGGCCGAGCTGGGCGGTGCCGCTCGGCCGGTGCGACTCGACGACGGCGAGCCGCAGCGAAGCGAACAGCGACCTGCCGGGGCCGGGGAGCAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA