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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

Basic information

species Oryza sativa
transcript LOC_Os01g57220.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
------------------------------------------------------------ccctaagattttgttcttgt----tgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaact-tggccgtttgaaa-----tgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
                                                                || ||  ||||  |||    ||||  | ||| ||   |  | |      |||| ||  ||  |      |   || |||  | |    |||   ||     | ||||||||||||||||| |||||||||||||| || ||||| |||||||| || ||||| || ||||||||||||||    |||||||||||||||  | | |
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaacatggtgtttctgtctcatgcatcataatctctctttaagt------ttcaattattctagaagagagctgttttgagatattattgttctgaacttgtttcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 12
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaat--gcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
            ||| || |   | ||  | |    |  |||     |||        | || |    | |   | |||   ||  | ||| || |  |||||||||||| ||||| |||||||| ||||| |||||||| |   | || |||||||| ||  | ||  | ||||   | ||  | | | |  ||   | | 
------------gtttttatcatattagcactgtaacaccaacatattctcttgaagttacttgagtctttttgtttgattatgtgcttttaaattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTGCAGTTTTAAAGCGTGAGGCTGCGAGAGGGACAATGATGGCAGCTCTATAACATGGCACTTACA

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
------------ccctaagattttgttcttgttgcaataaaattt-ccgctgcaatgc-tgtcttcattttctcctgggagatgtc-attctgaacttggccg-tttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
              ||   | |||    |  |   ||  | ||   || |     ||  || | | |||| ||   |  | |  || | ||     ||    | ||||  || ||||||||||||||||| |||||||| ||||| |||||||||||||||||||| || || ||  | || || |||||  | ||  | ||||  | |      |
gtttgattacacttcttgaactttacaatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgtttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA12G32860.1 (Glycine max), 3'ss of exon 10
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
            ||| ||  |      ||| |    || | ||| ||  |||  ||    || |  | | || || |  || |     ||  | | |||||||||||||||||| ||||| || ||||| |||||||| | |||||  ||||| || || |  || || |||||  | ||  |                 
------------gtttttaatagtcctaaact----ctaccatggtgcattctcttggctctagt-gttttctttgttgacatttaatttatatacgcagCAAGTATACATGTACTTCCGGGGCAGTGGAAAGGCTGCAGCGATGAGGCGTGAAGCTGCGCAAGGGGCCATGAGGGCAGCTCTA----------------

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA12G11820.2 (Glycine max), 3'ss of exon 12
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctga-acttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
      | |||| |  |  |  || | ||  |  |   | ||| ||  ||  | || ||  || |   | |  ||     | |||    | |    ||||||||||||| ||||| |||||||| ||||| |||||| | |   | ||||||||||| ||  | ||  | ||||   | ||  | ||| |  ||   | | 
------gtttttataatattaacacttaatctaacttggtaattct-cctgaagttact--tgtgtctttttgtttgactatttgattttatattttgcagCAAGTATATATGTACTTCCGTGGCAGTGGCAAGGCTACAGTTTTAAAACGTGAGGCTGCCAGAGGCACAATGATGGCAGCTCTATGACATGGCACTTACA

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
-----ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
          | || |   | || ||| ||        |   |   |   || ||  |  |   |   | | ||||    ||    |||   ||||| | | ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |  ||||| ||  | || ||  ||||  | ||    |||             
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactgaacataaccaaagtacatgtt-cactttttttgtttgtttgca-tacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
-----------------------ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
                        || |  || ||   |   | |||  |  ||||    ||| ||| | || | ||    | |          |   || |  |     |||||  || ||||||||||||||||| ||||| || ||||||||||| |||||||||||||| ||||| ||  | || ||  ||||  | ||  | ||||  | | |  | |
gtttgactacacttcttgaactttccaatcatcttaagcacat-gcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcact-atttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
------ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgt-cattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG-
         ||    |   |  || | | ||    |  | |   ||| |  || ||  |  |   |   |   |||| || | |    ||||  |      || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| |  ||||| ||  | || || |||||    ||  | ||||| |  | ||| | 
gttcgaatatacatctgaatatttttggaaagtggaaatacttagcact-ttgactgaacataaccaaagttaatgttcactttttgtttggttgc-----atacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATA-AATTACTTTGT

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcatt-------ttctcctgggagatgtcattctgaacttg-gccgttt-----gaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
  | ||  | |  |||   || | |  ||         |||  |||  ||    |       |    |  | || | |  |||     ||  |  ||||     |   ||||||||||||| ||||| ||||| || ||||| || || ||||||||||| ||||| || ||  | || || |||||  | || || | |    ||   | | 
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

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|25803449|gb|CA759418.1|CA759418
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTAAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGGAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|86258735|gb|CI065088.1|CI065088
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|87035348|gb|CI189970.1|CI189970
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|89180045|gb|CI044324.1|CI044324
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|55412661|gb|CV725037.1|CV725037
EST:     GATTTGGACTGTTTTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|86889655|gb|CI299853.1|CI299853
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|86866030|gb|CI336785.1|CI336785
EST:     GTTCTGGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GTTCT-GCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|3760903|gb|C98157.1|C98157
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|88225943|gb|CI225859.1|CI225859
EST:     ACTGTTCTGCCTTGAATCACTACTCAGCTTTGTTGTCATCCAG                         CAAGTATACAGGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: ACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|33683758|gb|CF311997.1|CF311997
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
EST: gi|88988413|gb|CI037656.1|CI037656
EST:     GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAG                         CAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT
genomic: GATTTGGACTGTTCTGCCTTGAATCACTACTCAGCGTTGTTGTCATCCAGgtgagtttta ... tgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG
                                           tttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcattttctcctgggagatgtcattctgaacttggccgtttgaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT