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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

Basic information

species Oryza sativa
transcript LOC_Os01g73130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA13G03470.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------aga---aaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgca----ttacgaattacgaattgatggat------gaaatttggttata-attttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
                                                                           |||   |    || | ||  ||   |   |  ||  | |  | || |  | ||| |      |||  ||||  || ||||  ||      |   |||  || ||   || | ||| ||||| |||||||| || |||||   ||| || || |||||||||   ||||| |||||| |||||||||||||||||||||||||||||||||||||
gttcgtcactctctttttatttgtaaaattttattcaatataacgataacaataataataataatattagggtctagatctatcgtagttggttgaacagttattgtaaaaacctttttgtacctgtcttcgattgctacagattaaaaaatgatttattctgtggctgttttattttatgattggtagGTATGGGAGCGGCGTATGGAACGGCGAAGAGTGGGGTGGGGGTGGCGTCGATGGGAGTGATGAGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G05630.2 (Glycine max), 3'ss of exon 1
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
  ||  ||  | |  |  ||     |        |   ||| ||  |  |   |             ||        |    | | || |  |||| |||| ||||| ||||||||||| || ||   ||||||||||||||| |||   ||||| |||||| ||||||||||||||||||| |||||||||||||| ||
gtaactaactaactcatcaaatcaaagagttttttttgtct-catttcccgaaaccgtcgtcgttttatcttaaaccgtgtgtcgtttttgttttttcagGTATGGGCGCGGCGTACGGCACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G23990.1 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------------agaaaaaaagatcgtaaaaagctcgatca--aacgatcga------tctgcaagtt-tctgcattacgaattacgaattgatgg--------atgaaatttggttataat----tttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
                                                                    |  |  ||  ||  ||  |||||| | |   |   || ||      ||||  |  | |||   ||||| ||||  ||   |||          ||   |||  || || |    || | ||| ||||| ||||||||||| |||||   ||| || || |||||||||   ||||| |||||| |||||||||||||||||||||||||||||||||||||
gttcgccactctctctatctctctctttttgtttataattttttatttaatttaacgataacaacaatactactaataataataccaagctctagcgtgagttattgaaaactttctgttatctgtctttgttacggattaaaaaaatatgatttattccgtggcctttatttttattatgattggtagGTATGGGAGCGGCGTACGGAACGGCAAAGAGTGGGGTGGGGGTGGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G24220.1 (Glycine max), 3'ss of exon 1
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaa-------ttgatggat--gaaat------ttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
             ||||  | ||| ||||||  |  ||  |     ||| |   |||| | || ||||       | | |  ||  ||||       | | || |  |||| |||| ||||| ||||||||||| || ||   ||||||||||||||| |||   ||||| |||||| ||||||||||||||||||| |||||||||||||| ||
-------------gtaactaactc-atcaaatcaaagagtttttttttttttttttacaatttccgaaaccggcgtcgttttatctgaaaccgtgtgtcgtttttgttttttcagGTATGGGAGCGGCGTACGGAACCGCGAAGAGCGGCGTCGGGGTTGCGTCGATGGGCGTGATGAGGCCGGAGCTGGTGATGAAATCGATCGTGCCGGTTGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0038g00790.t01 (Vitis vinifera), 3'ss of exon 1
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaat-tgatgga-tgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
|    | ||  || |      ||   |||     || ||   |     |    ||   ||  | ||| | |||| || ||   |||  ||||||||||  ||| ||||| || ||||| || |||||   ||| |||||||| ||||||   ||||| |||||| ||||||||||||||||||||||||| || || || ||
attcgataatttcttctccttcttcttcattttctcaataaccggacatagatatatagatcttcgattctgattgactgttgttt--ttataatttttgagGTATGGGAGCTGCGTATGGAACGGCGAAGAGTGGCGTCGGAGTGGCGTCGATGGGAGTGATGAGGCCGGAGCTGGTGATGAAGTCGATTGTACCAGTTGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 3'ss of exon 1
agaaaaaaagatcgtaaaaagctcgatcaaacgatc----gatctgcaagtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
   ||  |    |||  |  ||          | |     |  ||   |    ||   |  |   ||||  ||   |  |    |   |||| |      ||||||||||| || || || || || ||   ||| || || || |||||   |||||| ||||||||||| |||||||||||||||||||||||||| |||||
---aagcagtgacgttgagggcctatcttgttgttttgaaggactttgatcagcttgctcgctctttaccgatatgttaacccgaggaggtttttgagc-gcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCAGTGGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 1
--agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatgga-tgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
  ||   | |||||  | |       | | ||       || || |   |  |     ||    |      |||   |  |    |||||| | |||   |||||||||| || || || || || ||   ||| || || || |||||   |||||| ||||||||||| ||| |||||||||| || |||||||| || ||
gtagcgtacaagattttcaccgtgcagtttaattttcttatttggagcgtgattttgaacttcctggactctgacaaagcggtggttggttttgatt---cagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCAGAGTTGGTGATGAAATCTATCGTGCCAGTAGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 3'ss of exon 1
agaaaaaaagatcgtaaaaagctcgat--caaacgatcgatctgcaa----gtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
   || |  |||  |    | | |  |  | |  |    ||||   |    |  ||   ||| | |  || ||||  |  | ||||    |||| |      ||||||||||| || || || || || ||   ||| || || || |||||   |||||| ||||||||||| ||||||||||||||||||||||| || |||||
-ataacagcgatgttgggcaccccactttcgagtgcctcatctaggatatggcctcgaaattcctagatatgaataaaatggtgaa----ggtttttgcgc-gcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTACCAGTGGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatggatgaaat-ttggttataattttg-cagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
       ||    ||      ||  | |      |   || || ||  |  | | | ||||   |      ||| |  |||| |||  | | |||  | |||||||||| || || || ||||| ||   ||| || || || |||||   |||||| ||||||||||| |||||||||||||||||||||||||| |||||
-cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcg-acttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------------agaaaaaaagatcgtaaaaa-gctcgatcaaacgatcgatctgcaa--gtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
                                                                                    |     |  | |  |   ||         ||||     ||| |   |  |   ||| |||      ||||      |    | |||   |   |||||||||||||| || || || || || ||   ||| || || || |||||   |||||| ||||||||||||||||| |||||||| ||||||||||| |||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgagatttcgatcccaaaattccccattttcttatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCATCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

upper sequence: LOC_Os01g73130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------------------------------------------------------------agaaaaaaagatcgtaaaaa-gctcgatcaaacgatcgatctgcaa--gtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
                                                                                    |     |  | |  |   ||         ||||     ||| |   |  |   ||| |||      ||||      |      |||   |   |||||||||||||| || || || || || ||   ||| || || || ||||||  |||||| ||||||||||||||||| |||||||| ||||||||||| |||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgatatttcgatcccaaaattccccattttctcatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCGTCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT
                     aattgat  putative branch site (score: 4)
                              atgaaatttggttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaaaaagatcgtaaaaagctcgatcaaacgatcgatctgcaagtttctgcattacgaattacgaattgatggatgaaatttggttataattttgcagGCATGGGGGCGGCGTACGGGACGGCTCGGAGCGGCGTCGGGGTGGCGCACATGGGGGTGATGCGGCCGGAGCTGGTGATGAAGTCGATCGTGCCGGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- aaaaaaa
- - - - - - -gtaaaaag
- - - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - -atctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgatgg