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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataccatcattacacttggtactgaagtactgagtgggattttctccatagttggcttgtttttcatatgtatttaattttcctgtttgttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATGATGGAGACTGTTAGGAGTAAATGTATCACTCAATTACTGCTACTTGGGG

Basic information

species Oryza sativa
transcript LOC_Os07g37750.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37750.1 (Oryza sativa), 3'ss of exon 26
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 27
--cataccatcattacacttggtactgaagtactgagtgggattttctccatagttggcttgtttttcatatgtatttaattttcctgtttgttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATGATGGAGACTGTTAGGAGTAAATGTATCACTCAATTACTGCTACTTGGGG---
  |  | |     | ||   ||||   | | ||    |   | | |  | |   |     |  |  |  | | |  |     ||  || ||||| ||| | ||| ||||||   || | |||||||||  |||| || ||||| |  ||||||||||| ||||| ||||| |||||||| || || |||||||| |||||||   
aactcatctggcatccaaaaggtagccatgaac-atttcttagtgtgcctagtatgaaagtactgatattttctcctctggctttgtgcttgtttatcta-gGCCCCTGAT---GATGAGGCTGACAAGGCTGAAGAGGAAGAAAGCCCTATGATGGAAACTGTCAGGAGCAAATGTATTACACAGTTACTGCTGCTTGGGGCAA
















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|33688751|gb|CF316990.1|CF316990
EST:     CCAAATCAAAAGGTCGTACAGACGATATTGTGCCACCCTCACCTGTGAAG                         GCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATG
genomic: CCAAATCAAAAGGTCGTACAGACGATATTGTGCCACCCTCACCTGTGAAGgtacatgttt ... ttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATG
EST: gi|44667159|gb|CR280593.1|CR280593
EST:     CCAAATCAAAAGGTCGTACAGACGATATTGTGCCACCCTCACCTGTGAAG                         GCACCTGATGCTGACGGGGCCGACAAAACTGACGATGAAGAGAATCCTATG
genomic: CCAAATCAAAAGGTCGTACAGACGATATTGTGCCACCCTCACCTGTGAAGgtacatgttt ... ttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccatagttggcttgtttttcatatgtatttaattttcctgtttgttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATGATGGAGACTGTTAGGAGTAAATGTATCACTCAATTACTGCTACTTGGGG
                                           tgttgat  putative branch site (score: 4)
                                 ttttcctgtttgtt  CT-rich tract
            ttgtttttcatatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cataccatcattacacttggtactgaagtactgagtgggattttctccatagttggcttgtttttcatatgtatttaattttcctgtttgttgatcgaagGCACCTGATGCTGACGGGGCTGACAAAACTGACGATGAAGAGAATCCTATGATGGAGACTGTTAGGAGTAAATGTATCACTCAATTACTGCTACTTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
catacca
- - - - - - - - - ggtactg
- - - - - - - - - - - - - - - ctgagtg
- - - - - - - - - - - - - - - - - - - - - - ctccata
- - - - - - - - - - - - - - - - - - - - - - - - - - -tggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtat