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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaacaagtgcaaggctgctttcaagtgtctttttgcagataatgctagcaaggcaatgtgggtaaatttgctctaattttcttgacgatgttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGATCCAAGGTGGTCTGGGCGCAGCTTTTCCTTCTCACGCCACCTTCCCCCA

Basic information

species Oryza sativa
transcript LOC_Os01g65550.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G005236_T01 (Zea mays), 3'ss of exon 2
agaacaagtgcaaggctgcttt-caagtgtctttttgcagataatgctagcaaggcaatgtgggtaaatttgctctaattttctt----gacgatgttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGATCCAAGGTGGTCTGGGCGCAGCTTTTCCTTCTCACGCCACCTTCCCCCA
    ||  |||  |  |  ||   ||||| ||| |  | ||||||  ||||||| ||||||||||||| |||||||   ||| ||    || ||||||||||||||||||||||||| |||||  |||||||| || || |||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||||||| ||
---gcacatgcctgtttttttaataagtgccttctc-ctgataatattagcaag-caatgtgggtaaaattgctctctctttttttgctgatgatgttgctacagGAGGGGCTAGGAACTTTAAAGTGATGAAATCTTTCAGCCAGCAGGCAGGAATCCAAGGTGGACTGGGCGCAGCTTTTCCTTCTCATGCCACCTTCCCTCA

upper sequence: LOC_Os01g65550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G019266_T01 (Zea mays), 3'ss of exon 2
agaacaagtgcaaggctgctttca--agtgtctttttgcagataatgctagcaaggcaatgtgggtaaatttgctctaattttcttgacgatgttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGATCCAAGGTGGTCTGGGCGCAGCTTTTCCTTCTCACGCCACCTTCCCCCA
    ||| | |  |  |  ||| |  |||| ||| |  | ||||||  ||||||| |||||||||||||||||||    ||||  ||| ||||||||||||||||| ||||| | |||||| || ||||| ||||| | |||||||||||| ||||||||||| || |||||||||||||||||||| ||||||||||| ||
gacgcaaatacctgttttttttaattagtgccttctc-ctgataatattagcaag-caatgtgggtaaatttgcttctgttttgctgatgatgttgctacagGAGGAGCTAGAAACTTTAGAGTAATGAAATCCTTCAACCAGCAGGCAGGAATCCAAGGTGGACTCGGCGCAGCTTTTCCTTCTCATGCCACCTTCCCTCA
















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|58593494|gb|CF991802.1|CF991802
EST:     TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAAGCCCACAGCATG                         GAGGGGCTAGGAG
genomic: TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAACCCCACAGCATGgttagacatt ... gttgctacagGAGGGGCTAGGAG
EST: gi|58671703|gb|CK060389.1|CK060389
EST:     TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAACCCCACAGCATG                         GAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGA
genomic: TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAACCCCACAGCATGgttagacatt ... gttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGA
EST: gi|58606623|gb|CK034656.1|CK034656
EST:     TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAACCCCACAGCATG                         GAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGA
genomic: TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAACCCCACAGCATGgttagacatt ... gttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGA
EST: gi|58666021|gb|CK054707.1|CK054707
EST:     TCTGGCTTCCCTTGGGGTTCAGAGCTCTAGGCCTCCAACCCCACAGCATG                         GAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTT
genomic: TCTGGCTTCCCTTGGGGTTCAGAGATCTAGGCCTCCAACCCCACAGCATGgttagacatt ... gttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcaaggcaatgtgggtaaatttgctctaattttcttgacgatgttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGATCCAAGGTGGTCTGGGCGCAGCTTTTCCTTCTCACGCCACCTTCCCCCA
                                   tcttgac  putative branch site (score: 3)
                             taattttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaacaagtgcaaggctgctttcaagtgtctttttgcagataatgctagcaaggcaatgtgggtaaatttgctctaattttcttgacgatgttgctacagGAGGGGCTAGGAGCTTTAGGGTGATGAAGTCCTTTAGCCAGCAGGCAGGGATCCAAGGTGGTCTGGGCGCAGCTTTTCCTTCTCACGCCACCTTCCCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - -gtgcaag
- - - - - - - gctgctt
- - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - -tgctagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtg