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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttttttgtggaacctgagaagttgttttgatgtgttacctgggtaatcaatctcattgcaaattctgtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAATGAGAAGATGCGCGGCATTCTCATCGATTGGCTGATAGAG

Basic information

species Oryza sativa
transcript LOC_Os06g51110.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G073671_T01 (Zea mays), 3'ss of exon 6
--gtaacttt---tttgtggaacctgagaagttgttttga-----tgtgttacctgggtaatcaatctcattgcaa-attctgtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAATGAGAAGATGCGCGGCATTCTCATCGATTGGCTGATAGAG
     ||| |    || || | |  |   |||| |||| |       || | |  |  |    |||||||   ||| ||||||||| ||||||||   ||||| ||| || | ||||| ||||  ||||||| ||| ||||||||||||||||| |||||||| || || ||||| ||||||
gtacgactctgaccttctgaacctagtagagttattttcaattaccctgctgctggcatttgtaatctcaccacaacattctgtgtacacagGGTGCAAGCTGCGTCCCTACAAATTATATGTCAAGCCAAACTGATATAAATGAGAAGATGCGTGGCATTCTAATTGACTGGCTCATAGAG
















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|58685982|gb|CK074669.1|CK074669
EST:     CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
EST: gi|27577632|gb|CB000327.1|CB000327
EST:     TATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: TATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
EST: gi|25801281|gb|CA757242.1|CA757242
EST:     CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
EST: gi|58661172|gb|CK049852.1|CK049852
EST:     CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGC
genomic: CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGC
EST: gi|58652652|gb|CK041332.1|CK041332
EST:     CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
EST: gi|58653513|gb|CK042193.1|CK042193
EST:     CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
EST: gi|27576878|gb|CA999572.1|CA999572
EST:     CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: CAGTAGTTGAATATGTTGATGAAATTTACAGCTTCTACAGGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
EST: gi|58679267|gb|CK067954.1|CK067954
EST:     GGAGGAGTGAG                         GGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT
genomic: GGAGGAGTGAGgtaacttttt ... gtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttgatgtgttacctgggtaatcaatctcattgcaaattctgtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAATGAGAAGATGCGCGGCATTCTCATCGATTGGCTGATAGAG
   ttttgat  putative branch site (score: 4)
                      taatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacttttttgtggaacctgagaagttgttttgatgtgttacctgggtaatcaatctcattgcaaattctgtgtgcacagGGTTTGAGCTGTGTCTCTCCTAATTACATGTTGAGCCAAAATGACATAAATGAGAAGATGCGCGGCATTCTCATCGATTGGCTGATAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT