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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT

Basic information

species Oryza sativa
transcript LOC_Os02g04490.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 15
gtgtgttggtgcttctcacttttgttccgtcaccttg---ccttgtgcttgatc---tggaataacaccctgaccacttacggaaacta-------------tacactatgca--gGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
|| |||    ||    || |    |  | ||  ||||   |  || | || |       |  || ||     | |    | | || ||              || ||||||||  ||||||| |||||||||||  |||||||||| ||||| ||||||||  |||||||||||||||| ||||| |||||||| |||||||| || ||||| || 
gtttgtccacgccctcca-tcccatctcatcctcttgtgtctctgcggtttactactcagtgtagcattgccatctgcgatgtaacctgatcccgcctgtggtaaactatgcacagGGATCTGAAGGAGCATCTCAGAAGGTTGCAGCAGCAGTCTGATTCCCGGAGGAGGGCTGCTGTGAATGAGATGATGAGGCAGAGAGCGGCGGAAGTGGCC

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 15
gtgtgttggtgcttctca-cttttgttccgtcacct-tgccttgtgcttgatctggaataacaccct-----------gacc--acttacggaaactatacactatgca--gGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
|| |||||  |   |||  ||||||| |    || | ||  || ||  |   || | ||| ||               ||||  | ||||        || ||||||||  ||||||| |||||||||||| |||||||||||||||| |||||||| ||||||||||||||||| |||||||||||||| || ||||| || || || |||
gtttgttgtcgtccctcctcttttgtgcacatacatatggtttctgtgttcacttgtatagcattgccgtctgcgatagacctgatttacctgtgtggtaaactatgcacagGGATCTGAAGGAGCATCTTAGAAGGTTGCAACAGCAGTCTGATTCCAGGAGGAGGGCTGCTGTGAATGAAATGATGAGGCAAAGAGCGGCGGAGGTCGCT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA15G00250.1 (Glycine max), 3'ss of exon 16
----gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
    ||| ||  |   |   || |    || | | |  |  |  | |   |  | ||     | | | |   |  ||  ||    || |       ||| ||| | || || ||  |  | |||||||| || || |||||||| ||  | || ||||||||||  || |||||||| |||||||| ||||||||||| 
gtttgtgggtcaggcataggcattgcaattac-ttaagtcactgtttatatattttgcgtgtataacattttctttttggg---ttaaat------cagAGATTTAAAAGAACACTTAAGGAGGTTGCAGCAACAGTCTGATTCAAGACGAAGAGCTGCTGTAATGGAGATGATGAGGCAGAGAGCTGCAGAAGTTGCC

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 18
----gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
    ||   |  |   ||  || | || |   || | ||  | || |  | ||| | | ||   |     ||   |||       || |       ||| ||| | ||||| |||||  | ||| |||| || || ||||||||  || | || |||||||| |  ||||||||||| |||||||| ||||||||||||
gtttgtagatcaggcattgccaatattctcgagttaact--cttttttatagattttgtatg-tattaacactgtttatttgggttaaat------cagAGATTTAAAGGAACATCTAAGGAGGCTGCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTGATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 16
----gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
    ||   |  |   ||  || | || |   || | |   |  | |  | ||| | | ||   |     ||   |||       | || |     ||| ||| | || || |||||  | ||  | || || || ||||||||  || | || ||||||||||  ||||||||||| |||||||| ||||||||||||
gtttgtagatcaggcattgccattattctcgtgttaac--actattttatagattttgcatg-tattaatactgtttatttgggtt-taaat----cagAGATTTAAAAGAACATCTAAGGAGACTTCAGCAACAGTCTGATTCACGGCGTAGAGCTGCTGTAATGGAAATGATGAGGCAGAGAGCCGCAGAAGTTGCT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 17
-----------gtgtgttggtgcttctcacttttgttcc-gtcaccttgcct-tgtgcttgatctggaataacaccc-tgaccacttacggaaactata---cactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
              ||    | | ||   |||   ||   | |      | | | || |  || ||   |        ||| || |      | || |    | || | |||||| || |||||||||||  |||| || || |||||||| |||||  || | || || |||||||  |||||||||||||| ||||| |||||||| |||
gtaaacaaacctcatgaaattacatcaaccttacatttaagacgtgaaacatatttggtccatttgattttgtgttgatgatcattgtgaacatctctgtctctctgttcagGGACCTAAAGGAGCATCTGAGAAGATTACAGCAGCAATCAGATTCACGGCGCAGAGCAGCTGTAATGGAAATGATGAGACAAAGAGCTGCAGAAGTCGCT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 16
-----gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
      | | || |  |       |    |   |  |   |   |||      ||       |  |     |    | |  | || | | | | || |||||| || ||||| |||||  ||||||| ||||||||||| ||||||||| |||| ||||| || |  || ||||||||||||||||| |||||||| |||
tttggatatattagaaccggggcataacatatggcaaagcttttttgaaaaaaatggtccgcatgatttgtattgatcattgtaaatcttctcaattcagGGACCTAAAGGAACATCTGAGAAGGTTACAACAGCAATCAGATTCTAGGCGGAGAGCTGCCGTCATGGAGATGATGAGACAGAGAGCTGCAGAAGTCGCT

upper sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 15
gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctgga-ataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
    ||| ||  || |||  ||     |    || |      |  |   | || | || |||     | |   |||   | || ||    || ||| ||||| ||||||||| |  | ||| |||| ||||| |||||||||||| | || |||||||| |  || ||||||||||||||||| ||||| ||||||
----gtttgtagttgtcaacttgtggtcaatgccatcttaaatattgtctatgaatatcacatataaatcttatactttatct-taactcattcagAGATCTGAAGGAGCATTTGAGGAGGCTGCAGCAGCAGTCTGATTCTAGGCGAAGAGCTGCTGTGATGGAGATGATGAGACAGAGAGCTGCAGAGGTTGCT

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|29675948|gb|CB672223.1|CB672223
EST:     CAGGATGCAACGTGCCGAGATGCAG                         GGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAG
genomic: CAGGATGCAACGTGCCGAGATGCAGgtgtgttggt ... cactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAG
EST: gi|218499047|gb|FG943117.1|FG943117
EST:     CTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAG                         GGATCTCAAGGA
genomic: CTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAGgtgtgttggt ... cactatgcagGGATCTCAAGGA
EST: gi|29675947|gb|CB672222.1|CB672222
EST:     CTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAG                         GGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAG
genomic: CTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAGgtgtgttggt ... cactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAG
EST: gi|31818556|gb|CD645553.1|CD645553
EST:     CTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAG                         GGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAG
genomic: CTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAGgtgtgttggt ... cactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAG

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: 74 (upstream exon), 73 (downstream exon)
Score: 23

GTGCTTCAGGAGGGTGTGTTCTTTGCAAGAAAATGTGGTACATGCTCCAGCTCCATGCCCGAGCTTGCAGGGACTCAGGATGCAACGTGCCGAGATGCAGgtgtgttggt ... cactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT
                            cacttac  putative branch site (score: 23)
                                     aaactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttggtgcttctcacttttgttccgtcaccttgccttgtgcttgatctggaataacaccctgaccacttacggaaactatacactatgcagGGATCTCAAGGAGCATCTTCGAAGGTTGCAACAGCAATCTGATTCTAGGAGGAGGGCTGCTGTAAATGAAATGATGAGACAGAGAGCAGCAGAAGTTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT