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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcttgtctgccccacttgcatcccttcttttctgtaactgaaattttgtggtacattatgttagtatatattgtctgacgttgtggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

Basic information

species Oryza sativa
transcript LOC_Os01g19694.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G087741_T01 (Zea mays), 3'ss of exon 4
cgcttgtctgccccacttgcatcccttcttttctgtaactgaaattttgtggtacattatg-ttagtatat-attgtctgacgttgtggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
 |  |||  || |        |   ||         ||    ||  |   ||| || | ||   |||   | ||  ||||| | |||| ||||||    ||||| ||||| ||| ||||||| ||||| | ||| ||||| ||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||| |
-gtatgtaggcgctggccat-tttttttcaccaaacaatctgaacctgcaggtgcactgtgaccagtgactgataatctgatgctgtgctgctga----cagGAGGAAGACAAGGTGAGGCTCGCAGCAATGACCGGTCTCGACCCGAAGCAGATCAACAACTGGTTCATCAACCAGAGGAAGAGGCATTGGAAGCCATCTG

upper sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G41610.1 (Glycine max), 3'ss of exon 4
cgcttgtctgccccacttgcatcccttcttttctgtaactgaaattttgtggt--acatta-tgttagtatatattgtctgacgttgtggtgctgattga--cagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
   |  |  |    | |  ||    ||    ||| ||||  | | |  ||  |  |||||  | ||     | |    |   | |  | ||  | | |||  ||||| || || ||  ||| | |  |||  |  || ||||| || | |||||||||||| |||||||||||||| ||||| ||  |||| ||||| ||  | |
---taattagtt--attctcacaaattgcactctataacaaagactaggtaattaacatttctctttaagcaaaagacccagcctatttgttatcaatgatacagGAGGAGGAGAAAGTGAAGTTATCAGAAATTACTGGTCTGGATCAAAAGCAGATCAATAATTGGTTCATCAATCAGAGAAAACGGCATTGGAAACCTACCG

upper sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G39040.1 (Glycine max), 3'ss of exon 4
cgcttgtctgccccacttgcatccctt----cttttctgtaactgaaattttgtggtacattatgttagtatatattgtctgacgttgtggt-gctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
 |   || |  |  | |||||  |  |     || | | |||   |||    |    |   ||| ||  | |  ||    |||   |||  |   ||||  ||||||||| || ||  ||| | |  |||  |  || || || || | |||||||||||| |||||||||||||| ||||| ||  | || ||||| ||| | |
-gtgggtataacaaa-ttgcactctataacatttctatttaagcaaaagaccgatccagcctat-ttgatgtgaatgccttgaaactgttatcaatgat--acagGAAGAGGAGAAAGTGAAGTTGTCAGAAATTACTGGACTGGATCAAAAGCAGATCAATAATTGGTTCATCAATCAGAGAAAACGTCATTGGAAACCAACTG

upper sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0060g01180.t01 (Vitis vinifera), 3'ss of exon 4
-cgcttgtctgccccacttgcatcccttcttttctgtaactgaaattttgtggtacatt-atgttagtatatattgtctgacgttg--tggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
     |   |     | ||| ||       |  || |  |||  |   |    ||| || || |  | | |  |  |||||    |  || || ||||  ||||||||| || ||  ||| |||  ||| |   || || || ||||  |||||||| ||||| |||||||| |||||||||||| |||| ||||| ||||| |
aaaagttcatattggagttgtatttagaactg-ctatcgctgggacacttgtttactttcatttctggacacgt-atctgaaaaggattgatgatgat--acagGAAGATGAGAAATTGAAGCTATCAGAGGTTACTGGACTAGACCAGAAGCAGATTAACAACTGGTTCATAAACCAGAGGAAGCGGCATTGGAAACCATCAG

upper sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ23803 (Selaginella moellendorffii), 3'ss of exon 4
----------------------------------cgcttgtctgccccact-tgcatcccttcttttctgtaactgaaattttgtggtacattatgttagta--tatattgtctgacgttg---tggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                                   |  | |||  | |  | ||  |        | |  |  ||    |  |    |   |  | ||  |   | | || | |||| ||    | ||  || | |||||||  |  | |||  ||  || ||       || || || |||||||||||||||||||| ||||| || |||||| | ||| |||||||||| ||   ||
gtgagtacctttgtgttctttcttgttggcattctgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcatcgcttttttctttgacatttgcttcgttgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGGCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCGCAGG

upper sequence: LOC_Os01g19694.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ21443 (Selaginella moellendorffii), 3'ss of exon 5
----------------------------------cgcttgtctgccccact-tgcatcccttcttttctgtaactgaaattttgtggtacattatgttagta--tatattgtctgacgttg---tggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                                  ||  | |||  | |  | ||  |        | |  |  ||    |  |    |   |  | ||  |   | | || | |||| ||    | |   || | |||||||  |  | |||  ||  || ||       || || || |||||||||||||||||||| ||||| || |||||| | ||| |||||||||| |||  ||
gtgagtacctttgtgttctttcttgttggcattccgtgtctctttctcgttatggctagtgggcgtgccatggctttgttccttctttgtgtccttttcattgcttttttctttgacatttgcttcgctgtgctggacagGAGAACCAAAAGTCGAATCTCGCGCAATCCACCGGCCTGGACCCAAAGCAGATCAACAACTGGTTTATAAACCAGCGAAAGCGGCACTGGAATCCACAGG

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|88990744|gb|CI108131.1|CI108131
EST:     CACACACTACCGCTGGCCATATCCCACG                         GAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCCAAGCAG
genomic: CACACACTACCGCTGGCCATATCCCACGgtaatatgat ... tgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAG
EST: gi|27554393|gb|CA998293.1|CA998293
EST:     CGGCACTGCTTGAATGGTGGAACACACACTACCGCTGGCCATATCCCACG                         GAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAG
genomic: CGGCACTGCTTGAATGGTGGAACACACACTACCGCTGGCCATATCCCACGgtaatatgat ... tgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtggtacattatgttagtatatattgtctgacgttgtggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG
                                          tgctgat  putative branch site (score: 3)
       tacattatgttagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcttgtctgccccacttgcatcccttcttttctgtaactgaaattttgtggtacattatgttagtatatattgtctgacgttgtggtgctgattgacagGAAGAAGATAAGCTGAGGCTTGCAGCGAGGACAGGTCTTGACCCAAAGCAGATCAACAATTGGTTCATCAACCAGAGGAAGAGGCACTGGAAGCCATCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - tgtctgc
- - - - - - - - -tgcatcc
- - - - - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggtgc