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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacaactgttatagcttaccttgaaatgcttgtttttttttccttttttatatgttattctgatggacgtttctgtataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G085747_T01 (Zea mays), 3'ss of exon 15
gtatgacaactgttatagcttaccttgaaatgcttgtttttttttccttttttatatgttattctgatggacgtttctgtataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG
||||||||||  ||       ||||| || |  |||  ||||              |||| | ||||| || |||| |    || |||| || |||||||| ||||||||||||||||| |||||| || ||||||||||||| ||| |||||||||||||
gtatgacaaccttt------caccttcaagtatttggctttt-------------gtgttttactgatagaagtttttccgaaaatcagGATTGGTTTAGGTGCCCTTCTTTCAGGTGCCCGGCATGTTTCAGATGGCATGCTTCAAGCAGCAGCTGAGTG
















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|58596497|gb|CK007025.1|CK007025
EST:     GGTAGACAAGGGTACGCTAATCAAGCAAACAACATGTATCTGTTTCCTGG                         TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
genomic: GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaac ... tataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
EST: gi|58610908|gb|CK038620.1|CK038620
EST:     GGTAGACAAGGGTACGCTAATCAAGCAAACAACATGTATCTGTTTCCTGG                         TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
genomic: GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaac ... tataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
EST: gi|29664102|gb|CB660377.1|CB660377
EST:     GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGG                         TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
genomic: GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaac ... tataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
EST: gi|29615205|gb|CB620218.1|CB620218
EST:     GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGG                         TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
genomic: GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaac ... tataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
EST: gi|29671881|gb|CB668156.1|CB668156
EST:     GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGG                         TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
genomic: GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaac ... tataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
EST: gi|29662805|gb|CB659080.1|CB659080
EST:     GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGG                         TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT
genomic: GGTAGACAAGGGTACGCTAATCAAGCAAACAATATGTATCTGTTTCCTGGgtatgacaac ... tataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttttttccttttttatatgttattctgatggacgtttctgtataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG
                           ttctgat  putative branch site (score: 3)
                                       tttctgt  putative PPT
     ttttttccttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacaactgttatagcttaccttgaaatgcttgtttttttttccttttttatatgttattctgatggacgtttctgtataattcagTATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA