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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgcatacataaaatttgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTCTCAAACAACCTACAAATACTTGTGTCTTCAGGGGCTGATGCACAG

Basic information

species Oryza sativa
transcript LOC_Os01g15020.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 19
gtactgcatacataaaatttg-cacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTCTCAAACAACCTACAAATACTTGTGTCTTCAGGGGCTGATGCACAG
||  |  || | |||  | ||   ||   | |  ||   |||  |||| | |||||    |  ||| ||||    | |   ||||| ||||||  | | ||||| ||||||| |||||||||||| ||||| ||||| | ||||||     ||||||| |||||||| || |||||||||
gtgataaatgcctaatctatgatgcagtttatggttctgtgaatcatttc-attcagcctt-ctgacctttggggttt---cagGTAAAAACTGAACTCAAAGGACATCAAAAGAGGATAACTGGGTTGGCATTCTCCACCAACCTTGGCGTACTTGTTTCTTCAGGCGCCGATGCACAG

upper sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 21
gtactgcatacataaaatttg-cacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTCTCAAACAACCTACAAATACTTGTGTCTTCAGGGGCTGATGCACAG
||| |   |   |||  | ||   ||   | | |||   ||   |||| | |||||    |  ||| ||   |||  ||| ||||| ||||||||| | ||||| |||||||||||||||||||| ||||| ||||| | ||||||    |||||||| |||||||| ||||||||||||
gtaatcagtgtctaatctctgatgcagtttatgattctgtggatcatttc-attcagcctt-ctgacct---tttggttttcagGTAAAAACTAGACTCAAAGGACATCAAAGGAGGATAACTGGGTTGGCATTCTCCACCAACCTTGGCATACTTGTTTCTTCAGGCGCTGATGCACAG
















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|86860682|gb|CI324949.1|CI324949
EST:     TATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|58694171|gb|CK082858.1|CK082858
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|29625565|gb|CB630576.1|CB630576
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|58680385|gb|CK069072.1|CK069072
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|58611343|gb|CK039055.1|CK039055
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|33795487|gb|CF323613.1|CF323613
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|88828342|gb|CI000451.1|CI000451
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|29619450|gb|CB624462.1|CB624462
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
EST: gi|163927986|gb|EG712962.1|EG712962
EST:     TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAG                         GTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC
genomic: TTGGAATGGAAGATTCAACCATCCATATATACAATGTCAGGGTAGATGAGgtactgcata ... ttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatttattgagccattgctattcatttatattgagctttattttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTCTCAAACAACCTACAAATACTTGTGTCTTCAGGGGCTGATGCACAG
                                      ctttattttctttcc  CT-rich tract
                          atttatattgagcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgcatacataaaatttgcacatactgtaatttattgagccattgctattcatttatattgagctttattttctttccagGTCAAAACTAGATTGAAAGGGCATCAAAGGAGGATAACTGGTTTGGCCTTCTCAAACAACCTACAAATACTTGTGTCTTCAGGGGCTGATGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT