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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagggttcttctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA

Basic information

species Oryza sativa
transcript LOC_Os07g37780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G019325_T01 (Zea mays), 3'ss of exon 2
gtagggttcttctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA
||  |    |  |||   ||| ||||||| | |  || |||| || |  | || |  | ||  |   |||||  |  |||||||||||||||| ||||||||||||||||||||||||||||||||||| || || |||||||||||||||||||| |||||||| ||||||||||||||||||
gtgagagattcttgcctcttccatgctttctattctcagtgaacaatatagattttgtgacagtagatttcttttaaattttagCTCAAAGAAATCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAATCGATTTTGGAAGAGCATTGGCCTTGGTTTCAAGACTCCCAGGGAAGCAATTGAA

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G044800_T02 (Zea mays), 3'ss of exon 2
gtagggttcttctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA
||  |    || |||   ||| |||||||    ||| | |||||| |  |||| |  | ||  |   | |||   |  || |||||||||||| || ||||| ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||
gtgagaactttttgcctcttccatgctttca--attttctgagcaatatacattttgtgacagtagatatcttaatt-ttatagCTCAAAGAAATCCGGCAAAGGTAAGAAGCCTGGCAAGGGCGGCAACCGATTCTGGAAGAGCATTGGCCTTGGCTTCAAGACTCCCAGGGAAGCAATTGAA

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G23400.2 (Glycine max), 3'ss of exon 2
---------------gtagggttcttctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgat-gtt-tttctgcttcatttt--agCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA
               |      |  |   || ||    |  ||  | | | |  || |  |||   |||    | || | ||| ||| || | | |||   ||| |||||||| |||| ||||| ||||  || || || ||||| |||||||| ||||||  |||||| ||||| || ||||| ||||||||||| || |||
gtacgcttagtgttcgagaaaatgcttcacttttgttgtttttgttttttccattgtgatgttttgatgctgaatcgtttgttgtttttggtccctttcgcagCACAAAGAAGACTGGGAAGGGAAAGAGACCTGGAAAAGGTGGGAACCGCTTTTGGAAGTCCATTGGGCTTGGATTTAAGACTCCCAGGGAAGCCATCGAA

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 2
------------------gtagggttcttctgctctttcaatgctt-tatgtattctgtgagcagttcaca-tgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA
                  | |   ||   ||  | |||||  | |  || || |    |  |    | | | | |||||| || |   ||   |||   |  ||||||||||||   || ||||| |||| ||| || |||||||| || || |||||||||||||||||  | || || ||||| ||||| || |||||||||
atatacctaatagaacttggaatatttcccttttttttcatggttgataagtgtgtcatttgtgtcttaaagtatcttaatga-gcaattgaactt---tgcagCTCAAAGAAGGGCGGAAAGGGAAAGAGGCCTGGAAAGGGTGGAAATCGATTCTGGAAGAGCATTGGATTGGGATTTAAGACACCCAGAGATGCAATTGAA

upper sequence: LOC_Os07g37780.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtagggttct-tctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgatgtttttctgctt------cattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA
                            | || || | | |  ||  |    | |     | || |        || |   || || ||  | ||| ||||         || |  ||||| ||||| ||||  ||||| |||| ||| || |||||||| ||||| |||||||||||||||||| | || || ||||| ||| | || || ||||||
gtaacagaaaattacgaatacattctcattggtttttgttttttcccttggggatgacattgtttttcccctttttaattcgtttttaccgtttttctctgtgctgaaaacaatccagCTCGAAGAAATCTGCGAAGGGGAAGAGGCCTGGGAAGGGTGGAAACCGGTTCTGGAAGAGCATTGGCTTAGGGTTTAAGACACCCCGAGACGCTATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtattctgtgagcagttcacatgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA
                         tcttaac  putative branch site (score: 2)
                                    tttttctgcttcattt  putative PPT
                                             ttcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagggttcttctgctctttcaatgctttatgtattctgtgagcagttcacatgtcttaacgatgtttttctgcttcattttagCTCAAAGAAGTCTGGCAAGGGTAAGAAGCCAGGCAAGGGTGGCAACCGCTTCTGGAAGAGCATTGGCCTTGGCTTCAAGACCCCCAGGGAAGCAATTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA