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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtacacacacaactctgcagatcgatttgcagatgaaaattattgcagcaacatctgactcatctcattgatctccataactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC

Basic information

species Oryza sativa
transcript LOC_Os08g39300.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G137868_T04 (Zea mays), 3'ss of exon 2
----gtcagtacacac----acaactctgcagatcgatttgcagatgaaaattattgcagcaacat---ctgactcatctcattgatctccataactctg-cagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC
      || | || |      ||| ||     ||  |||      || ||  || |  | |   ||   |  |  |||    ||  | ||     || || ||||||||| |  ||||    ||||| || ||||||||||||||||||||  | || ||||| ||||| || ||   ||||||||| || |||||||||||||
gtagcgcactgcagagtttggcaattcgtttaattaattaatcagtgcaacgtactatatcttgatgctcccaaacattatttttttttcttcttctttgtcagCTGCAACTTCTGGGATGTCTGAGCGGTGTGGAGATGGTGCTCAAGGATGTGGGGTACCCAGTGAAACTAGGTAGCGGCGTGGCAGCCGCGGCGGCGTACC

upper sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G119511_T01 (Zea mays), 3'ss of exon 1
---------gtcagtacacacacaactctgcag----atcgatttgcagatgaaaattattgcagca----acatct-gactcat--ctcattgatctccataactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC
           ||| ||      |  | |  |     | | ||| |   || |  || | |||| ||    | |||| || | ||  | ||    | | | |   |   ||||||||| || ||||    ||||| || ||||||||||||||||||||  | || ||||| ||||| || ||   |||||||||||| |||||||||||||
gtagtgcactgcaggacgggttgagttatataataatagcaattcgttaatta--atcactgcaacatactatatcttgaatgatgccccaacatttttccttctttgtcagCTGCAACTGCTGGGATGTCTGAGCGGTGTGGAGATGGTGCTCAAGGATGTGGGGTACCCAGTGAAACTAGGTAGCGGCGTGGCGGCCGCGGCGGCGTACC

upper sequence: LOC_Os08g39300.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G359559_T01 (Zea mays), 3'ss of exon 1
-----------------gtcagtacacacacaactctgcagatcg----atttgcagatgaaaattattgcagcaacatctgactcatctcattga---tctccataactctg-cagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC
                   |  |||    | |  |  |||  |||    |||      || ||  || |  | |      |||  |  |  |   |   ||| |    || || ||||||||| |  ||||    ||||| || ||||||||||||||||||||  | || ||||| |||||||| ||   |||||||||||| |||||||||||||
gtagtgcactgcagggttgcgttaccgttatatattggcaattcgtttaattaatcagtgcaacgtactatatcttgtcttgatgctcccaaaaaaaattcttctcttctttgtcagCTGCAACTTCTGGGATGTCTGAGCGGTGTGGAGATGGTGCTCAAGGATGTGGGGTACCCAGTGAAGCTAGGTAGCGGCGTGGCGGCCGCGGCGGCGTACC

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|16753675|gb|BM038054.1|BM038054
EST:     GCAAGNTGTTCAGGATC-GCCACCTCGGCCACCTCAACGAG                         CTGCTATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: GCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|33800871|gb|CF326308.1|CF326308
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|16578334|gb|BI812429.1|BI812429
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|33797701|gb|CF324709.1|CF324709
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|18385541|gb|BM418740.1|BM418740
EST:     A-GTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|33381048|gb|CF196391.1|CF196391
EST:     AGGTCGCCGGCAAGGTGTTCNNNNTCGGCNACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGT
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGT
EST: gi|8956848|gb|BE230651.1|BE230651
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGA
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGA
EST: gi|4715918|gb|AU057034.1|AU057034
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|16577686|gb|BI811781.1|BI811781
EST:     A-GTCGCCGGCAAGGTGTTCAGGATC-GCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|14981844|gb|BI306522.1|BI306522
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|8956425|gb|BE230228.1|BE230228
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAA
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAA
EST: gi|16579460|gb|BI813555.1|BI813555
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTC-GCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
EST: gi|58688176|gb|CK076863.1|CK076863
EST:     AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAG                         CTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC
genomic: AGGTCGCCGGCAAGGTGTTCAGGATCGGCCACCTCGGCCACCTCAACGAGgtcagtacac ... aactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaaattattgcagcaacatctgactcatctcattgatctccataactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC
                                         ccataac  putative branch site (score: 3)
     attatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtacacacacaactctgcagatcgatttgcagatgaaaattattgcagcaacatctgactcatctcattgatctccataactctgcagCTGCAATTGATGGGTGCCCTGAGTGGAGTGGAGATGGTGCTCAAGGACATCGGCTACCCGGTGAAGCTCGGCTCCGGCGTGGCGGCGGCGGCGGCGTACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC