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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATGACATGTATCTGAAACGCTTCACTCAACGAGAGCATAGAGTGGCTGCAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgttttcaattgcatgttttctgttcctttggttttagcattcctgtttaactcgtctaaattagctaaagaacatgttactggaagtagttgt...

Basic information

species Oryza sativa
transcript LOC_Os07g49460.3
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g49460.4 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G005732_T03 (Zea mays), 5'ss of exon 4
CAATGACATGTATCTGAAACGCTTCACTC--AACGAGAGCATAGAGTGGCTGCAG-TGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgttttcaattgcatgtt------ttctgttcctttggttttagc-attcctgtttaactcgtctaa--attagcta-aagaacatgttactggaag-tagttgt-------------
   |||||  ||| | | |||  |  ||   | |  ||    |         ||| | |  || | |||| |||||| |||||| || ||||| || ||||||||||||||||||||||||||| ||      |  | ||  |||| ||| |        |||||||   |    |  ||| | || ||| ||  ||| ||    | | | |||             
---TGACACATATGTCAGACGGCTTGCTGCGAGCATGACACCACGACAAGAACAGCTAAAGAAATATAGAGAGAAAAAGAAAGATCGGAACTTTGGGAAAAAGgtagcctgttttcaattgcatattaatatttattctttatttgttttcaattgcatatgtttaagaagagagagcattggatagaaggactggtttctttctgatggctgtctgccatttccag

upper sequence: LOC_Os07g49460.4 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G033962_T01 (Zea mays), 5'ss of exon 7
CAATGACATGTATCTGAAACGCTTCACTC--AACGAGAGCATAGAGTGGCTGCAG-TGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgttttcaattgcatgttttctgttcctttggttttagcattcctgtttaactcgtctaaattagctaaagaacatgttactggaag--tagttgt---------------------------
   |||||  ||| | | |||  |  ||   |||  ||              ||| | |  || | |||| |||||| |||||| || ||||| || || |||||||||||||| ||||||||| ||   | ||| | |   |||    |   |     |   || |||         ||| |||   |  ||| |  | |||                             
---TGACACATATGTCAGACGGCTTGCTGCGAACATGACACCGCGACAAGCACAGCTAAAGAAATATAGAGAGAAAAAGAAAGACCGGAACTTTGGGAAGAAGgtagcctgtttgcaattgcatcttaatttttcttctttatttgttttcagttacatatatgtttaagaagaagtgagagcattggataggaggactggtttctttctgatggccgtctgccattttcag
















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|88688484|gb|CI732060.1|CI732060
EST:     CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|218479723|gb|FG953390.1|FG953390
EST:     CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|25799920|gb|CA755881.1|CA755881
EST:     CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|88691241|gb|CI733825.1|CI733825
EST:     CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|58670257|gb|CK058943.1|CK058943
EST:     CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|88728157|gb|CI751667.1|CI751667
EST:     CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|86858976|gb|CI275166.1|CI275166
EST:     AGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: AGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|38478820|gb|CF962953.1|CF962953
EST:     AAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTA-CAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: AAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|86479559|gb|CI122192.1|CI122192
EST:     GATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: GATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
EST: gi|38475943|gb|CF960076.1|CF960076
EST:     CAGTGATCAAGTTTAGACAGAAAAGGACAGAGCGCAACTTCGGAAAAAAG                         GTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC
genomic: CAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgtt ... ccattttcagGTGCGGTACCAGAGCAGAAAGAGGCTGGCCGAGCAGCGGCCAAGGGTCCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATGACATGTATCTGAAACGCTTCACTCAACGAGAGCATAGAGTGGCTGCAGTGATCAAGTTTAGACAGAAAAGGAAAGAGCGCAACTTCGGAAAAAAGgtagcctgttttcaattgcatgttttctgttcctttggttttagcattcctgtttaactcgtctaaattagctaaagaacatgttactggaagtagttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA