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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGAATACTTTTTCCGGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccctctttatcaccttcctcatggctcacctatgtagcaaattgttctgcgtttctaaattcaacagtaacatgttgacaacttgatattagat...

Basic information

species Oryza sativa
transcript LOC_Os01g55500.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55500.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G437859_T04 (Zea mays), 5'ss of exon 13
CGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGAATACTTTTTCCGGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccctctttatcaccttcctcatggctcacctatgtagcaaattgttctgcgtttctaaattcaacagtaacatgttgacaacttgatattagat------------
|||||| ||||||||||| |||||||| || || || |||||||||||||| |||| |||||| ||||| ||||| ||||||||||| ||||||||||||||| ||| || | | |   |  ||   |   |  |||   | ||    | | | |    || ||    | | |  |||||         ||  |||  ||            
CGTCGGCGTCTCCATCTTCCTTGGCCTGTCCGTCCCGGAATACTTTTTCCGCTACACCATGGCTGCTCATCGTGGTCCTGCGCACACGAAAGCTGGATGGgttcgtctctgtctctttgcccccatttcaatatcct-catggctccatctccaggtcgtcaaacagtacctgagacatgacc-tgggctgggattgaatcatgaatggcag

upper sequence: LOC_Os01g55500.1 (Oryza sativa), 5'ss of exon 13
lower sequence: PP1S228_5V6.1 (Physcomitrella patens), 5'ss of exon 12
CGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGAATACTTTTTCCGGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccctctttatcaccttcctcatg-gctcacctatgtag-caaattgttctgcgtttctaaattcaacagtaacatgttgacaacttgatattagat------------
  | |||||||||||||| |||||||| |||||||| || |||||       |  |   ||   |||  || ||| ||||  |||||   |||| ||||||| |||||         |  |     |||   |   || | ||  |   |||| ||   | |    || |     ||    ||   || ||     ||  ||            
AATTGGTGTCTCCATCTTCCTTGGCCTCTCTGTGCCAGAGTACTTCAGAGAATTTACAGTGCGTGCTGGGCATGGTCCTGTCCACACTGGAGCTCGATGGgtatgtcctaaacagaaatttcttagatgtaattcactgtatactcgctttgtactcgctctacttatcctgttatatttggtactcacctcaccgttccatgccatgtatcag
















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|89186694|gb|CI114403.1|CI114403
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88203426|gb|CI203275.1|CI203275
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|25807066|gb|CA763027.1|CA763027
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCTCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88970709|gb|CI385379.1|CI385379
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88222923|gb|CI220669.1|CI220669
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|15852172|gb|BI804968.1|BI804968
EST:     GGTACAGCAT-GCCGCTCAGCGTGGCCCTGCGCACAC-AAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCTCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88838577|gb|CI375125.1|CI375125
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|87026155|gb|CI256898.1|CI256898
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|86873801|gb|CI341234.1|CI341234
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|58670557|gb|CK059243.1|CK059243
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCTCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88437904|gb|CI536063.1|CI536063
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88460448|gb|CI531921.1|CI531921
EST:     TGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: TGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88845862|gb|CI084592.1|CI084592
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88304565|gb|CI518221.1|CI518221
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
EST: gi|88414210|gb|CI533580.1|CI533580
EST:     GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGG                         TTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG
genomic: GGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccct ... tataatgcagTTCAACGACTACATCAACACTATCTTCTCATCGCCTCCGACGGTCGGACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCGGTGTCTCCATCTTTCTTGGCCTATCTGTGCCCGAATACTTTTTCCGGTACAGCATGGCCGCTCAGCGTGGCCCTGCGCACACAAAAGCTGGATGGgtttgtccctctttatcaccttcctcatggctcacctatgtagcaaattgttctgcgtttctaaattcaacagtaacatgttgacaacttgatattagat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA