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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttttccttacactttctgctattctgtacgttgttactattgttcatatatactgtagccttatctaactctccctgaaccttttttttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCGATTCCTTCGCGAAGAAAGCGCAGATGTACTACCAGAGGCGTCCAATGCT

Basic information

species Oryza sativa
transcript LOC_Os01g07360.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07360.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G831408_T01 (Zea mays), 3'ss of exon 2
------tatttttccttacactttctgctattctgtacgttgttactat-tgttcatatatactgtagccttatctaactctccctgaaccttttttttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCGATTCCTTCGCGAAGAAAGCGCAGATGTACTACCAGAGGCGTCCAATGCT
      || |  | ||| || | |  |  |   ||||  |    ||| | || |  | | |  ||  || | ||| |    |||||||||     |      ||||||||||||||||||||||||||||||||| ||||| || |||||||| ||||| |||||||| ||||||||||| ||||| |||||||||||||| |||||
ccaaagtaatgctgcttgca-tataagaaagcgtgtat-tacccactgtgtgatgctgttttttggtgcttcatcaattcttccctgaac-----tgaaacatgcagAAATGGACAAGCAAGTGAAGGAAATGCTCCAGCTGATCGAGGAGGACGGCGACTCCTTCGCTAAGAAAGCGCAAATGTATTACCAGAGGCGTCCGATGCT
















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|58666269|gb|CK054955.1|CK054955
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|58672522|gb|CK061208.1|CK061208
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|58653981|gb|CK042661.1|CK042661
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|88407696|gb|CI607830.1|CI607830
EST:     CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGA
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGA
EST: gi|33677737|gb|CF305976.1|CF305976
EST:     CAGTCACATTAGCCCTAAGAACCCT-AATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAATGATATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|58671469|gb|CK060155.1|CK060155
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|58606805|gb|CK034838.1|CK034838
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGC
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGC
EST: gi|58663083|gb|CK051769.1|CK051769
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|33797289|gb|CF324507.1|CF324507
EST:     CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|58662899|gb|CK051585.1|CK051585
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
EST: gi|58664309|gb|CK052995.1|CK052995
EST:     TAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAG                         AAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG
genomic: CAGTCACATTAGCCCTAAGAACTCTAAATGGCTTGCAGAAAATCTTGAAGgtgagctgaa ... ttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatatatactgtagccttatctaactctccctgaaccttttttttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCGATTCCTTCGCGAAGAAAGCGCAGATGTACTACCAGAGGCGTCCAATGCT
                    atctaac  putative branch site (score: 2)
                          ctctccctgaaccttt  CT-rich tract
                                   aacctttttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttttccttacactttctgctattctgtacgttgttactattgttcatatatactgtagccttatctaactctccctgaaccttttttttttttgcagAAATGGACAAGCAAGTGAAGGAAATGCTGCAGCTTATTGAGGAGGATGGCGATTCCTTCGCGAAGAAAGCGCAGATGTACTACCAGAGGCGTCCAATGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG