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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgaccctctccctccctccctctcctcgcgctgcgctgtactgtacgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc...

Basic information

species Oryza sativa
transcript LOC_Os01g59440.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM5G815009_T01 (Zea mays), 5'ss of exon 1
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgaccctctccct-ccctccctc-tcctcgcgctgcgctgtactgtacgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc-
||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||  |   |||||  | ||||||| ||||||| |  | || | |  | || |   || |   |     |    | |  |   |||| ||||  |     
GGGACCCCGGCGGCGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACCCGCCTgtgagccgctgcctcccaactctccctcgtcctcgctcccccctttcccctgcg-gcccgcccccttcaataatcccttgacgg--ggggaaacttcagtatg

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G121820_T01 (Zea mays), 5'ss of exon 1
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgaccctctccctccctccctctc-ctcgcgctgcgctgtactgtacgcg-taggctcgagttgggtacttttgggtgtttgggggaactggatcgc
||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||   || | ||   |  | ||| | ||  | | || |  |      ||||    | | |||| |||  |     || || |||  |    | ||   
GGGACCCCGGCGGCGTTCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACCCGCCTgtgagccgtccccgcctctcaactctccctctttctcggccccttttcccccgcggcccgtttgagtcgggcccgccgtggcgtgtggatggggagcata--

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G44250.2 (Glycine max), 5'ss of exon 1
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc-ctctccctccctccctctcctcgcgctgcgctgtactgt-acgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc
 |||||| | |   || || ||||||||||| ||||| ||||| |  ||||| || |||||||||||||||||| |||  |||||||| ||||| ||  |||  ||  || ||||| ||| ||| |||||   |   ||  |  | |||| | ||       | | |||  |||| |  | |  ||      | |    |  
CGGACCCTGACAACGTCCTCCAGAGCTGGGATCCCACTCTCGTTAGTCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcctctctctctctctctctctctctgttttgttcctttctgtgatgcagctttcctaattgt-tactgtctgttactttaatttatttatact-

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA14G04520.1 (Glycine max), 5'ss of exon 1
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgaccctctccctccctccctctcctcgcgctgcgctgtactgtacgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc----
 |||||| | |   || || ||||||||||| ||||| ||||| | |||||| || |||||||||||||||||| |||  |||||||| ||||| ||| |||  ||  |||   | ||| ||   | |    | | || | |||    | |      | |    |  | |||||||   | |||     |     |||      
CGGACCCTGACAACGTTCTCCAGAGCTGGGATCCCACTCTCGTTAGCCCCTGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGCGTgtatgcatccc---ctctctctgtgtgtgtgtgtg-tgtgttgttgctttcttaattgttactatctgttacttttatttatttatattactgctatcagtttt

upper sequence: LOC_Os01g59440.2 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv08s0040g00520.t01 (Vitis vinifera), 5'ss of exon 1
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc-ctctccctccctccctctcctcgcgct-gcgctgtactgtacgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc
  || || | |   ||||| ||||||||||| || |  ||||||||||| || |||||||||||| |||||||  | |  |||  ||||||||| ||  |||  |    | || ||  ||     ||||| | |   | |    || |   |    |||| |  |  | |    ||||   | | |     |  |    |  
CCGATCCGGACAACGTGCTCCAGAGCTGGGATCCGAACCTCGTCAACCCTTGTACCTGGTTCCACATCACCTGTAATCAGGACGGCCGCGTCACTCGAGTgtatgtattctctatctttctgctactctcttagttttcgtttcgttcctgatatataggtttcatctcga-gtttttatttatatattt-atttctccctt

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|2317317|gb|C22371.1|C22371
EST:     CGACCGCGACAACCGCGTCACGCGCCT                         GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
genomic: CGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc ... cttctaacagGGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
EST: gi|29642936|gb|CB647943.1|CB647943
EST:     TGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCT                         GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
genomic: TGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc ... cttctaacagGGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
EST: gi|58597997|gb|CK008525.1|CK008525
EST:     TGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCT                         GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
genomic: TGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc ... cttctaacagGGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
EST: gi|58678911|gb|CK067598.1|CK067598
EST:     TGCACCTGGTTCCACGTCACCTGCGACCGCGAGAACCGCGTCACGCGCCT                         GGATCTTGGGAATTTGAACTTATCTGGGCATCTGGTGCCTGAGCTTGGAAA
genomic: TGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc ... cttctaacagGGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
EST: gi|218479908|gb|FG956823.1|FG956823
EST:     TGCACCTGG-TCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCT                         GGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA
genomic: TGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgacc ... cttctaacagGGATCTTGGGAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGACCCCGGCGGGGTGCTGCAGAGCTGGGACCCCACGCTCGTCAACCCCTGCACCTGGTTCCACGTCACCTGCGACCGCGACAACCGCGTCACGCGCCTgtgagcgaccctctccctccctccctctcctcgcgctgcgctgtactgtacgcgtaggctcgagttgggtacttttgggtgtttgggggaactggatcgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggggaa