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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttccttgaaacaatcttttctttccgggtcgtgtgacagatcacatttgagctttcctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcag

Basic information

species Oryza sativa
transcript LOC_Os12g03470.2
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G077299_T03 (Zea mays), 5'ss of exon 13
TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttccttgaaacaatcttttctttccgggtcgtgtgacagatcacatttgagctttcctgcgtagggctttat-taagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcag----------------------------------------------------
|||| ||||| || |||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||| |||| || ||  ||  ||| ||  || |  |||    |      | |    ||||  | |  |  ||    || |  |   ||||  |      ||  || | ||          | ||||   || |    ||                                                       
TTGTAAGTGAGTACGCTGTTTGGAGAGGTGATGCAGGTAGAGGAAGTCTTCTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgtgatctctcgtttgaa--atcattggtt-ctaggttaccttctgattaaaccctgagtctccgcggataatttttcacatgttatct-ttgctcgttgagatcacatgaccctacagagttctgcctgctctagtgtcactacgaagataatcttaaatgtgagttggtgaccttttgtttttatttgcag

upper sequence: LOC_Os12g03470.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G006130_T05 (Zea mays), 5'ss of exon 13
TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttccttgaaacaatcttttctttccgggtcgtgtga-cagatcac-atttgagctttcctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcag
|||| || || || ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||| |||| |||| |||||           ||  || |  || |  ||| | ||||   ||||  | |  |  || | ||| | ||       |||||| |||    | |      |||||||| | ||    |    | |||||||
TTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctcctt-----------ttggttgcaagttggttgatctgatccttattttcgttggcgggcttggggttcta-------ctactaccaaggatagtc-----tttactgtgagttag-atgacctttttgcag

upper sequence: LOC_Os12g03470.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G006130_T03 (Zea mays), 5'ss of exon 14
TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttccttgaaacaatcttttctttccgggtcgtgtgacagatcacatttgagctttcctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcag
|||| || || || ||||| ||||||||||| || |||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||||||||| |||| |||| |||||       |  || |     || || | |||     |  ||||  | |  |  || | ||| | ||       |||||| |||    | |      |||||||| | ||    |    | |||||||
TTGTGAGCGAGTACGCTGTCTGGAGAAGTGACGCGGGTAGAGGCAGTCTTCTTGCTTCGTTGGCTGAAGCTGCTTTCCTCACTGGTCTGGAGAAGAACAGgtgatctctcctt------ttggttgcaagttggttcatctgat---ccttattttcgttggcgggcttggggttcta-------ctactaccaaggatagtc-----tttactgtgagttag-atgacctttttgcag

upper sequence: LOC_Os12g03470.2 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G393002_T01 (Zea mays), 5'ss of exon 23
TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttccttgaaacaa-tcttttctttccgggtcgtgtgacagatcacatttgagctttcctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcag
||||||| || ||||| ||||||| || ||| || |||||||||| ||| || ||| ||||||||||||| |||||||||||||||||||||||||| ||||    | |  |  |   || |||   || |     |  ||||| || | | ||  || ||||  |   | |  ||||        |   |  | ||||   |    | ||| |  |  |                    
TTGTCAGCGAGTATGCAGTTTGGAAAACTGACGCCGGTAGAGGAACTCTCCTGGCTGCATTGGCAGAAGCGGCTTTCCTTACTGGACTGGAGAAGAACAGgtggcatataatatatttaaatctacactatttttttattgtga-agctaagat--gatcttttgt---tggttctttg-------ccttttgccaatgttgttgttttttttccttggcag------------------

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|29627660|gb|CB632671.1|CB632671
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
EST: gi|699908|gb|D46199.1|D46199
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
EST: gi|33654398|gb|CF277012.1|CF277012
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAAT-G                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
EST: gi|58690391|gb|CK079078.1|CK079078
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
EST: gi|29667818|gb|CB664093.1|CB664093
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCTTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
EST: gi|29686128|gb|CB682403.1|CB682403
EST:     CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAG                         TGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA
genomic: CTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttc ... ttctttgcagTGATGTTGTTCAGATGGCAAGTTATGCACCACTGTTCGTGAACAACAATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTCAGTGAATATGCTGTTTGGAGAAGTGATGCAGGTAGAGGAAGTCTACTTGCTTCATTGGCAGAAGCTGCTTTCCTTACTGGACTGGAGAAGAATAGgttatctttccttgaaacaatcttttctttccgggtcgtgtgacagatcacatttgagctttcctgcgtagggctttattaagatctactaacaaatgcaatgagatatttactgtaacttcttgttggttctttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA