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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttatctttcataatgaatttctgaaatgataatttatgagagtttatcttgcgtaccgaataaaatttctggtacattatttcaacccagaaattccaatgaatcactaatcttgtactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG

Basic information

species Oryza sativa
transcript LOC_Os10g11140.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 17
gtattttatctttcataatgaatttctgaaatgataatttatgagagtttatcttgcgtaccgaataaaatttctggtacat--tatttcaacccagaaattccaatg-aatcactaatcttgta-ctgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG
                                 |||||||  | |  | | |||| | ||   || ||     ||  | | |  ||  |   |  ||   ||    |  || || | || |||||  | |||||| |||||||||  | ||||||||  |||||||||| || ||||||||||| || ||||| |||||||||||||||||||| |
---------------------------------ataatttgagtgcatatttctt-cttaattaaaaagccacctaattcctcctaagttggctgagtttttttggtttaaccaatgattttgtaattctacagGCGTGTGAATCACACAGTGCAAACCAGATGATGGATCACCTTAGAGATGTTATGGCAAATAGCAAGCCTGGAGAGAAATACG
















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|89198777|gb|CI003514.1|CI003514
EST:     TATGATTATGAG                         GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
genomic: TATGATTATGAGgtattttatc ... tactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
EST: gi|24468739|gb|CA305688.1|CA305688
EST:     GGAATTTCTTCTCCAGATATGATTATGAG                         GAGTGTGAATCTGAGAGTTCAAATAAGATGATGGAGCATCTTAGAGATGTG
genomic: GGAATTTCTTCTCCAGATATGATTATGAGgtattttatc ... tactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
EST: gi|86892654|gb|CI312043.1|CI312043
EST:     CCACTGGGCAACCTATGGAAGGAATTTCTTCTCCCAGATATGATTATGAG                         GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
genomic: -CACTGGGCAACCTATGGAAGGAATTTCTTCT-CCAGATATGATTATGAGgtattttatc ... tactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
EST: gi|58611262|gb|CK038974.1|CK038974
EST:     AACACTGGGCAACCTATGGAAGGAATTTCTTCTCCAGATATGATTATGAG                         GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
genomic: AACACTGGGCAACCTATGGAAGGAATTTCTTCTCCAGATATGATTATGAGgtattttatc ... tactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
EST: gi|44665085|gb|CR278519.1|CR278519
EST:     AACACTGGGCAACCTATGGAAGGAA-TTCTTCTCCAGATATGATTATGAG                         GAGTGTGAATCTGAGAGTTCAAATAAGATGATGGAGCATCTTAGAGATGTG
genomic: AACACTGGGCAACCTATGGAAGGAATTTCTTCTCCAGATATGATTATGAGgtattttatc ... tactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
EST: gi|29681951|gb|CB678226.1|CB678226
EST:     AACACTGGGCAACCTATGGAAGGAATTTCTTCTCCAGATATGATTATGAG                         GAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG
genomic: AACACTGGGCAACCTATGGAAGGAATTTCTTCTCCAGATATGATTATGAGgtattttatc ... tactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtacattatttcaacccagaaattccaatgaatcactaatcttgtactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG
                                  cactaat  putative branch site (score: 2)
     attatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattttatctttcataatgaatttctgaaatgataatttatgagagtttatcttgcgtaccgaataaaatttctggtacattatttcaacccagaaattccaatgaatcactaatcttgtactgtacagGAGTGTGAATCTGAGAGTGCAAATAAGATGATGGAGCATCTTAGAGATGTGATCGCAAAAAGCAAGCCTGGAGAGAAATATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA