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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaggagcaaacataaatatttgtttctctatactataacattctacctgattcattattttaccacaactattggtctgatttatttttgtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 41
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 41
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 42
---------------------------------------------------------------------------taaggag-caaacataaatatttgtttctctatactataacattctacctgattcattattttaccacaactattggtctgatttat---ttttgttta-tgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG
                                                                           ||      || |  | || |||| ||    | || | | | ||| |     ||||| |  || | || ||  |||| |||||| |||   ||||||||  ||||||| |||||||| ||||||||||| |||||||||||||| ||||||| ||| ||||||||| |  | ||||| ||||| || |||||||||||||||||||
gtcatgctgttgatctcttcccatagttctcccacctgtctcacctccttgaggctccgtttttatttgtcacattattttttcacatgtcaagattttttaaaatctagtgttatatttt-ttacattcactccttaaacaaaaacattg-tctgatatatgccttttgttttctgcagTCCGTTGAAGGTATGAAAGTTATATGCCATGAGCTAACACAGGCAGCTGACCCTGAAAGCACATTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 41
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 24
--------------------------------------------------------------------------------taaggagcaaacataaatatttgtttctctatactataacattctacctgattcattattttaccacaactattggtctgatttatttttgt----ttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG
                                                                                | |       |||| |||||||      ||   |  |   ||  |   |   ||| | ||| | ||||   | ||||||||| ||| ||| |    || ||||||| |||||||| ||||||||||| |||||||||||||| ||||||| ||||||||||||| | || ||||| ||||| || |||||||||||||||||||
gtcatgctgttgatcacttcccatagtcctcccatagtcccatctgttccatcctttgaggctccatgtttatttttatattaatttttcacatcaatattttaaagcctg-gcggtgttatattttttacatcactctttaaacacatacactggtctgatatatgtttttagttttctgcagTCCGTTGAAGGTATGAAAGTTATATGCCATGAGCTAACACAGGCAGCTGATCCTGAAAGCACGGTGCTTGAAGATCTTATTAAGGAAGCTGACAGATTAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 41
lower sequence: GLYMA20G32430.1 (Glycine max), 3'ss of exon 43
--------------------------------------taaggagcaaacataaatatttgtt----tctctatactataacattctacctgattcattattttaccacaactattggtctgat----ttatttttgtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTT---GATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG
                                      |  |      | ||| |||| | ||    | | |   ||||    || |   |  || |  ||        |||| |   | | |     || ||||| ||  ||||||||||||| |||||||||||| | || |||||| || |||||||   |   ||||||||| |   ||   | ||||| ||  | || || || || ||     
gtgactagaatggctgatagttaaaacttactaatttttctgatttgtatatagatatatcttgagatttttcccctattctctttttggtttttgaaaatggaggttgaactttgattttcaaaatgtttttttttttggtgcagTCTGTTGATGGAATGAAAGTTGTTTGTCATGAGTTAGCTCAGGCCACTAGTGATCCTGAAGGAAGTGCTATGGATGAACTTGTGAAAGATGCAGATAGGC---

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 41
lower sequence: GLYMA10G35140.1 (Glycine max), 3'ss of exon 44
---------------------------------------taaggagcaaacataaatatttgtttctctatactataacattctacctgattcattattttaccacaactattggtct-----------gatttatttttgtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTT---GATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG
                                       |           ||| | || | | |||  | | | |  |  | | |    ||   | ||  |  |      |||  ||            ||| |||||| |   ||||||||||||| |||||||||||||| || |||||| || |||||||   |   ||||||||| |   ||   | ||||| ||  | || || || || ||     
gtgaatagaatgactgatagttaaaacttagcaacaattttcctgatttgtatatagatatatctcttgagattttccccctattctctttttggttttcaaaaatggaggttgaactctgatgttcaaaattaatttttttgggtgcagTCTGTTGATGGAATGAAAGTTATTTGTCATGAGTTAGCTCAGGCCACTAGTGATCCTGAAGGAAGTGCTATGGATGAACTTGTGAAAGATGCAGATAGGC---

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 41
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 3'ss of exon 13
taaggagcaaacataaatatttgtttc---tctatactataacattctacctgattcattattttaccacaactat--tggtctg-atttatttttgtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGT---TGATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG
        |  |  | || || | |||   | | | ||      || |   |   |  ||| ||       ||| |  |  |||| |  ||||||||    | |||||||||||||||||||||||| | ||||||||| |  | |||||      |||||| ||  |   ||   | |||||  |  | || || || || |||    
-----gatatccccatatcttagcttcatttttttcctcatctgttttttttccctttttagttggaagagactttcttattctgtaaatatttttggg-gtacagTCTGTTGAAGGAATGAAAGTTGTGTGCCATGAGTTGGCACAGGCGACCAGTGATCCAGAGGGAAGTGCAATGGATGACATTTTGAAAGATGCGGATAGAC---

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|33679052|gb|CF307291.1|CF307291
EST:     CAGATTGGCGTGAAGCTCTTGATATTGTTGCACTAGGTTTGCCTGAGCAG                         TCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGAT
genomic: CAGATTGGCGTGAAGCTCTTGATATTGTTGCACTAGGTTTGCCTGAGCAGgtcatgcttt ... gtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGAT
EST: gi|300216015|gb|HO088641.1|HO088641
EST:     CAGATTGGCGTGAAGCTCTTGATATTGTTGCACTAGGTTTGCCTGAGCAG                         TCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGAT
genomic: CAGATTGGCGTGAAGCTCTTGATATTGTTGCACTAGGTTTGCCTGAGCAGgtcatgcttt ... gtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgattcattattttaccacaactattggtctgatttatttttgtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG
                              gtctgat  putative branch site (score: 4)
                                        tttttgttt  putative PPT
                                 tgatttatttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaggagcaaacataaatatttgtttctctatactataacattctacctgattcattattttaccacaactattggtctgatttatttttgtttatgcagTCTGTTGAAGGAATGAAAGTTATCTGCCATGAGCTAACTCAGGCAGTTGATCCTGAAAGCTCTGTCCTTGATGATCTGATCAAGGAAGCTGACAGATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA