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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaattactcaagaatcttgtattccaaacgtttccttaggtttttgttaagaaaaacacgctgtatttcagagactactttctgttttctcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTCCACTCCCTGGTCGGGCAGTCAGCCTCGCCGGAATACCTTCAGAAGCTGA

Basic information

species Oryza sativa
transcript LOC_Os01g62070.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62070.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G014454_T01 (Zea mays), 3'ss of exon 5
--------agaattactcaagaatcttgtattccaaacgtttccttaggtttttgttaagaaaaacacgctgtatttcagagactactttctgttttctcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTCCACTCCCTGGTCGGGCAGTCAGCCTCGCCGGAATACCTTCAGAAGCTGA
         |   ||    |  |  ||| |||   ||| || |   |     |  || |      || | | ||| ||    | ||  |   ||  || |   ||||||| || |||||||||||||| |||||||||||||||||||| |||||||| ||||||||||| |||||||| ||||||||||| ||||| ||||| ||||
tgactcactgttctatggtaatactttgcatttgcaac-ttgcaagaaacactctttca-----tcatgatttatctccagaattaactgtcgtcctccc--ctgcagCTGGCGATCTACACGATCAGGACATGGTCGATGACGGTGCTGGAGAACGTGCACTCCCTGGTGGGGCAGTCGGCCTCGCCGGAGTACCTCCAGAAACTGA
















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|29661349|gb|CB657624.1|CB657624
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|33364700|gb|BP433013.1|BP433013
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATRTACACGATCAGAACATGGTCGAATGACGGTGCTCGAYAAACG
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCG-ATGACGGTGCTCGA-GAACG
EST: gi|38470206|gb|CF954337.1|CF954337
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29620907|gb|CB625918.1|CB625918
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29639091|gb|CB644100.1|CB644100
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29657119|gb|CB653394.1|CB653394
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29661350|gb|CB657625.1|CB657625
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|88380767|gb|CI634792.1|CI634792
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29675077|gb|CB671352.1|CB671352
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         ATAGCAATATACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29663340|gb|CB659615.1|CB659615
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
EST: gi|29688324|gb|CB684599.1|CB684599
EST:     TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATC                         CTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC
genomic: TACTAGCGACTTATATCGAAGGTTGGATCGACCCAGTTGGTGCAATCATCgtaagtacca ... tcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaagaaaaacacgctgtatttcagagactactttctgttttctcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTCCACTCCCTGGTCGGGCAGTCAGCCTCGCCGGAATACCTTCAGAAGCTGA
                              ctactttctgttttct  CT-rich tract
     agaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaattactcaagaatcttgtattccaaacgtttccttaggtttttgttaagaaaaacacgctgtatttcagagactactttctgttttctcgtttgcagCTAGCAATCTACACGATCAGAACATGGTCGATGACGGTGCTCGAGAACGTCCACTCCCTGGTCGGGCAGTCAGCCTCGCCGGAATACCTTCAGAAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - cttgtat
- - - - - - - - - - - - - - - - - - - - gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacgctg