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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattgcttgtaccttgctgtcaactgaagacctagataaagtttgttttttgggtttatgctgtctttagatgcactccttattcttctactacaattatactgttaagtgacaacgctttttattttatatgctaatatggggttcgcttcctttctattcag

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 17
AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattgcttgtaccttgctgtcaactgaagacctagataaagtttgttttttgggtttatgctgtctttagatgcactccttattcttctactacaattatactgttaagtgacaacgctttttattttatatgctaatatggggttcgcttcctttctattcag
||||| || ||||||||||| ||||||||||||||||||||||| |||||||||||||||||   || || |||| |  |||| |  | |      |     |  |     |     | | | |  |    | | |||    |   |||      ||  ||||  | |||     |                                                     
AATCTGTGTGTGACCGCAGCGCATTACCCCATTCGAGAAATCCTAGAGAAGGAAAAGAAGgtacacaatg-ttgt-ctctgcttttgattatccttcgcagcagggagcagt-----gatatgtttttctgtgaaatgatgcctacattgggtcgctg-aattccattgtgtgcag-----------------------------------------------------

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 26
lower sequence: GRMZM2G126453_T01 (Zea mays), 5'ss of exon 21
AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattgcttgtaccttgctgtcaactgaagacctagataaagtttgttttttgggtttatgctgtctttagatgcactccttattcttctactacaattatactgttaagtgacaacgctttttattttatatgctaatatggggttcgcttcctttctattcag
||||| || |||||||| || ||||||||||| |||||||| || |||||||||||||||||   || |||  || |  ||||      ||    |   | |     |||    |  | ||     || |   ||  | |      ||  ||  | ||    |  | | ||   ||   |  ||   |  |   | ||||    | |  |||  ||||  | | | |||
AATCTGTGTGTGACCGCGGCGCATTACCCCATCCGAGAAATTCTGGAGAAGGAAAAGAAGgtacacaatgcc-gt-ctctgcttctggttg----ctccgtttgcacttggcagtatgattatccttggcagcag--ggagcggcgatgtttgaatta----tgcatttttttctgttgagcctagatcatgactgtgctgggctcg--ttcaattccactgtgtgcag
















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|55409323|gb|CV721699.1|CV721699
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCC
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCC
EST: gi|58653111|gb|CK041791.1|CK041791
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|58691499|gb|CK080186.1|CK080186
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|7274059|gb|AU031974.2|AU031974
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|33659831|gb|CF282444.1|CF282444
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGC-AAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|29614541|gb|CB619554.1|CB619554
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|86480548|gb|CI123181.1|CI123181
EST:     CCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: CCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|8860068|gb|AU097386.1|AU097386
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|11171080|gb|AU163614.1|AU163614
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|29682150|gb|CB678425.1|CB678425
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|15857794|gb|BI810606.1|BI810606
EST:     TGACC-CAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGC-AAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|8860101|gb|AU097419.1|AU097419
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|86479265|gb|CI121898.1|CI121898
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCGTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|86849466|gb|CI299672.1|CI299672
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|5038858|gb|AU070968.1|AU070968
EST:     CAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: CAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|27554453|gb|CA998353.1|CA998353
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAGAATGTGGCAAAAGCATAACGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
EST: gi|58686681|gb|CK075368.1|CK075368
EST:     TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAG                         GAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT
genomic: TGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 53 (upstream exon), 53 (downstream exon)
Score: 5

AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattg ... ttctattcagGAGAAAAATGTGGCAAAAGCAGAAGGCAGGCCTGAGCCTGCATTGTATGGTAGTGAGGACATTCGTCCTCTGACCTTAGATGATTTCAAATCTGCCCATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCTATGCGTGACCGCAGCTCATTACCCCATTCGAGAAATCCTTGAGAAGGAAAAGAAGgttggcattgcttgtaccttgctgtcaactgaagacctagataaagtttgttttttgggtttatgctgtctttagatgcactccttattcttctactacaattatactgttaagtgacaacgctttttattttatatgctaatatggggttcgcttcctttctattcag

- - - - - - -  GCAGCT
- - - - - - - - CAGCTC
- - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG