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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 2
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G081322_T01 (Zea mays), 3'ss of exon 2
-------------------------------------gtatccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacgtacaagagtt--tctatccttttatgctg----ttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG
                                     | |  || |      |   ||    |||| ||||   | |||   | |     || ||   ||||||||    | ||  |||||| ||    |  || |||| | |  |  | || || ||||| |||||||||||  | ||||| ||||||||  ||||||||||| |||| || || ||||| |||  ||||||||| ||||||||||| |||
gtatccctactactaccataccagtagatggcttcatgcaagctgccacct-tattttagctgttttttttctctttctgtgtcttcggttccacacgcaagagttgtcttttctctttatgttggctatgtgctccttgacttgagcacagAGGGACAGAGATATGGAGGATCGAGGATTTCAAGCCAGTCGCTTTGCCAAAATCAGACTATGGCAAATTCTACTGTGGAGATTCTTATATAGTTCTGCAG

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G32010.1 (Glycine max), 3'ss of exon 2
--gta-tccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG
  ||| |   | || ||||      ||  || ||| ||||| | || || ||   |  |   || |        ||||   ||  |  |||     ||||  |    | ||| ||||| ||||||||||||||| | |||||| |||||||||| ||||| | | | || || || ||||| ||||  |||||||| || ||  |  | |||
atgtaattgatattcaaatataagcattatt-gttctagttatattattata---agttggatata-------ttatctacttgaggagttttagacttagctttt-tgtagAGGCACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGATCTGAATATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G29280.1 (Glycine max), 3'ss of exon 1
gtatccttctttaaatgcctttatggttt--gttttagttgtcttcttttagaaatctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG
         | ||| ||   ||    |||  |  ||| |  |||  || ||  | | || ||  || |  |  ||||   ||  |  |||     ||||| |    | ||| || || ||||||||||||||| | |||||| |||||||||| ||||| | | | ||||| || ||||| ||||  |||||||| || ||  |  | |||
--------atgtaattgatattcaaatttaagaattattgttctagttatattattataagttgaata--tattatctacttgaggagttttagacttaactttt-tgtagAGGGACTGAAATATGGAGGATTGAGGATTTTCAGCCAGTTCCATTGCCCAGACCTGATTATGGGAAATTCTACATGGGAGATTCTTACATCATCTTGCAG

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g08690.t01 (Vitis vinifera), 3'ss of exon 1
gtatccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacg--tacaagagtttctatcctt--ttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG
           |  |||| | | |    |||| | ||| |     || |  || || |   |     | || ||||  ||  || ||   ||     |||||  |   | ||||||||| ||||||||||| ||| |  | ||| |||||||||||||||||||  | ||||| |||||||| ||||  || || || || || || || |||
-----------tgcatgcatgtgtt-cctgttattgttctagatattgaacaagctgctattgtcttaattgctatttttgcttctggaattgtgaacttaac-atcttgtagTGGCACCGAAATATGGAGAATTGAGAACTTTCAGCCAGTTCCTTTGCCAAAGTCCGATTATGGTAAATTCTACACAGGGGACTCTTACATTGTCCTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG
 ccccttaat  putative branch site 
                                        ttaattaaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttctttaaatgcctttatggtttgttttagttgtcttcttttagaaatctacgtacaagagtttctatccttttatgctgttagccccttaattaaaatatagTGGCACAGAAATATGGAGGATTCAAGATTTTAAGCCAGTTCCTTTGCCAAAAGCAGATTACGGTAAATTTTACAATGGAGATTCATATATAGTTCTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT