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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattaatgacatgatatttgttggagtatacccaatctgcagaagcctcggctgataattgtttatccgataaccttaaatatgttctttttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACCAATGGTGCAG

Basic information

species Oryza sativa
transcript LOC_Os04g43750.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g43750.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G089767_T01 (Zea mays), 3'ss of exon 9
-----ttat-taatgacatgatatttgttggagtatacccaatct-gcagaagcctcggctgataattgtttatccgataaccttaaatatgttctttttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACCAATGGTGCAG
     ||||  | | |||  ||  || |     |  |||    || |  ||  |    | | ||  | |||   | || || ||||||||   |  |     ||||||| ||||| |||||||| ||| | ||||| ||||| |||||||||||||||||||||||||
gtcccttatacattcacaccattattctcctcttggaccttggctagttgagacaaatgtttatcctggttc--ctgaaaatcttaaatactatgct-----tgcagGTGAAAACTTTCCCTGTGATCCTCTTGCCTAAGGAGAAGCTTGTTGACACCAATGGTGCAG
















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|163922915|gb|EG712740.1|EG712740
EST:     CTGTCATTACTCAAGGCTGTGACCCAGTAGTTGTGGCTGATGATGGAAAG                         GTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
genomic: CTGTCATTACTCAAGGCTGTGACCCAGTAGTTGTGGCTGATGATGGAAAGgtaaatattc ... tttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
EST: gi|88246571|gb|CI246420.1|CI246420
EST:     CAGTAGTTGTGGCTGATGATGGAAAG                         GTCAAAACATTCCCTGTNATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
genomic: CAGTAGTTGTGGCTGATGATGGAAAGgtaaatattc ... tttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
EST: gi|88849633|gb|CI089739.1|CI089739
EST:     GCTGTGACCCAGTAGTTGTGGCTGATGATGGAAAG                         GTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
genomic: GCTGTGACCCAGTAGTTGTGGCTGATGATGGAAAGgtaaatattc ... tttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
EST: gi|86430015|gb|CI082438.1|CI082438
EST:     GTAGTTGTGGCTGATGATGGAAAG                         GTCAAAACATTCCCTGTAATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
genomic: GTAGTTGTGGCTGATGATGGAAAGgtaaatattc ... tttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
EST: gi|66921821|gb|CX108669.1|CX108669
EST:     CTGTCATTACTCAAGGCTGTGACCCAGTAGTTGTGGCTGATGATGGAAAG                         GTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC
genomic: CTGTCATTACTCAAGGCTGTGACCCAGTAGTTGTGGCTGATGATGGAAAGgtaaatattc ... tttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctcggctgataattgtttatccgataaccttaaatatgttctttttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACCAATGGTGCAG
                       cgataac  putative branch site (score: 3)
                                        ttctttttgct  putative PPT
                               ttaaatatgttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattaatgacatgatatttgttggagtatacccaatctgcagaagcctcggctgataattgtttatccgataaccttaaatatgttctttttgctgcagGTCAAAACATTCCCTGTTATCGTTTTGCCCAAGGAAAAGCTTGTTGACACCAATGGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - -acatgat
- - - - - - - - -tttgttg
- - - - - - - - - - - - - - - - - -atctgca
- - - - - - - - - - - - - - - - - - - - - - - - -cggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttctt