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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC

Basic information

species Oryza sativa
transcript LOC_Os03g27260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G26190.1 (Glycine max), 3'ss of exon 2
gtaatttctttggcaatttgctcca--tgattcttcaactgtcttgcta----tttaatgagttggatgactaagtt--tgtctgtttgt--acagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
|||   ||||| ||   |  |   |  ||  || ||     | |||||     |||||||| ||   |    |  ||  ||    ||||   ||||||||| ||||||||||| ||||| || |  ||||| |||||||| ||||| ||||| ||||| ||||| ||||||||| |||| ||||| || ||| | |
gtatgctctttagctgctaaccttaaatgcatcctctcaatttttgctgaatttttaatga-ttatctattcaccttcatgctcttttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACTGGAGGTTGTGACAAACAAGGATTCCCGATGAAACAGGGAGTGCTTACTCCTGGTCGTGTTCGACTTTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G08210.1 (Glycine max), 3'ss of exon 3
--------------gtaat--ttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtct---gtttg-----tacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
              | ||   |||  | |      | | | |||   | |    |      |  | ||||| |||| | |       | |||    ||||     ||||||||||||| |||||||| ||||| || |  ||||| || ||||||||||| || || |||||||| || ||| | ||  |||| ||||| |||||  | |
gtatggtttttgctggaacccttccatagtgcagagtttcctgaagttacctgagaaacattgatcaatga-ttggcttatccgtcctttcttatatttgctacttacagGAATTCAAAGGCTATGTCTTCAAAATTACTGGAGGTTGCGACAAGCAAGGATTTCCAATGAAGCAAGGAGTGTTGACCCCTGGTCGTGTTCGCCTCTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G45770.1 (Glycine max), 3'ss of exon 3
gtaatttctttggcaatttgctcca--tgattcttcaactgtcttgct-atttaatga--gttggatgactaagtttgtctgtttgt-----acagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
|||   ||||| ||   |  |   |  ||  || ||     |  |||| | || || |   ||   |    |  ||  |   | |||     ||||||||| ||||||||||| ||||| || |  ||||| |||||||| ||||| || || ||||||||||| ||||| ||| |||| |||||  | ||| | |
gtatgctctttagctgctaaccttaaatgtctcctctgaatttctgctgaatttataatgattatctattcaccttcatgactctgttgccaacagGAATTTAAGGGCTATGTCTTCAAAATTACCGGAGGTTGTGACAAACAAGGATTTCCAATGAAGCAGGGAGTGCTGACTCCTGGTCGTGTTAGACTTTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatttctttggcaatttgctccatgattctt-caactgtcttgcta-tttaatgagttggatg--actaagtttgtctg----tttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
|| |  | |||  |   | | ||  || || || |   |||||||  | || | |    |  |    | |  || ||| |     | | | |||||||||||||| || |||||||||||||||||||| |||||||||||||||||||| ||||| || || || || ||| | || |||||||| ||| | |
gtgaaatttttt-ctcctggttcagtgtttttttctgatgtcttgtgagttcagtatacttaacagaattgtgtgtgttttgagctatttgcagGAATTCAAGGGATACGTATTCAAGATCATGGGAGGATGTGACAAGCAAGGTTTCCCAATGAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTCTTTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G31700.1 (Arabidopsis thaliana), 3'ss of exon 3
------gtaatttctttggcaatttgctcca-tgattcttcaact--gtcttgctattta-atga--gttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
       |    | |||   | |||| || | ||| | |  |  |  |  || | |   | ||||   |    ||  || |  |   ||||  | ||||| ||||| || || || |||||||||| ||| || || || |||||||||||||| ||||||||||| ||  | ||| | || ||||| |||||| | |
gtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G31700.2 (Arabidopsis thaliana), 3'ss of exon 1
--------gtaatttctttggcaatttgctcca-tgattcttcaact--gtcttgctattta-atga--gttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
         |    | |||   | |||| || | ||| | |  |  |  |  || | |   | ||||   |    ||  || |  |   ||||  | ||||| ||||| || || || |||||||||| ||| || || || |||||||||||||| ||||||||||| ||  | ||| | || ||||| |||||| | |
aggtacagattccatttttcttactttgatctaatgagtgtgaagattagcatttcgaagcagatgatgatgttttgtttatgaattgttgttattgcagGAGTTCAAAGGATACGTTTTCAAGATCAAGGGTGGTTGCGATAAGCAAGGTTTCCCAATGAAGCAGGGAGTTTTGACTCCAGGCCGTGTTCGCCTTTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv18s0001g06290.t01 (Vitis vinifera), 3'ss of exon 3
----gtaatttctttggcaatttgct-ccatgattcttcaactgtcttgctat-ttaatgagttggatgactaagtttgtctgtttgt---acagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
    | | || |  | |  ||    | |||  |||||   ||| ||   |||  || ||        |   |  |||||| |||||||   ||||||||| || |||||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||| | ||| |||| |||||  | ||  | |
gtaagcatttaccattgttatgcaatgccaaaattct---actatcagactagatttatataacatttatttttgtttgtttgtttgtgtgacagGAATTTAATGGCTATGTATTCAAAATCATGGGAGGCTGTGACAAGCAAGGGTTCCCAATGAAGCAGGGAGTGTTAACTCCTGGTCGTGTTAGTCTCTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv07s0191g00060.t01 (Vitis vinifera), 3'ss of exon 3
--gtaatttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
   | ||||  ||   | | | ||        |||   || | ||   | | | | | |    |  || |    |  |||||| |||||| |||||||| ||||||||||| || |||||||||||||||||||||||||| || ||||||||||| || || ||  | || || ||||  ||||| |
gtatgattttgttactattcttcttaggataacttgccctttgttaggaatgatttattgatgtatcttaa---gcgtgtttg-acagGAGTTCAAGGGTTATGTATTCAAAATAATGGGAGGCTGTGACAAGCAAGGTTTTCCAATGAAGCAGGGAGTACTGACCCCAGGCCGAGTCCAACTTCTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0017g01350.t01 (Vitis vinifera), 3'ss of exon 3
gta-atttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
|||    | ||  ||  ||  | |  | |||  ||   | |  |   || || | | |   |  |   |  |  |||| ||  |||||| |||||||||||||| |||||||||||||| || |||||||||||||| || |||||||||||||| || || ||| |||| |||||  | ||| | |
gtatgccttttctgctcttctcccacttatttatctcatattgtttgatctact-aatcatacaaaacatgtcatctgctt-cacagGAGTTCAAGGGCTATGTTTTCAAGATCATGGGTGGTTGTGACAAGCAAGGGTTTCCCATGAAGCAGGGAGTACTGACTCCTGGCCGTGTTAGTCTTTTGC

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S253_38V6.1 (Physcomitrella patens), 3'ss of exon 2
----------gtaatttctttggcaatttgctccatgattcttcaactgtcttg----ctatttaatgagttggatgactaagtttgtctgtttgtacagG----AATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
          ||      ||  | |||  ||  | |   | | |  ||  | ||    || | | ||  ||     |  |   || ||   | ||| |||     ||||| | | | |   |||         ||   || ||||| |||  ||        | |||  |  |||  | |         | | | ||       
cagataggcagtgcgagattcaggaatgcgccacctttatatacgcctagcatgggagctctcttatcggtcttcggctttgtttggtgcttgtgttcagTCGCCAATTCTACGACAAGAGATTGGCCCAGGAGGTCAGCGGTGACCAGCTGGGAGATGAGTTCAAGGGGTATGTCTTCAAGATCATGGGAGGCTGCGAC----

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S311_33V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaatttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC---------
                                                              | |   | |   | | |||   | || |||||||| || || |||||||| |||||||| ||||||||||| |||||||||||||||||||||||  | ||    |||||||| |  || ||           
--------------------------------------------------------------gtcagtggtgaccagcttggtgatgagttcaagggatacgttttcaagattatgggaggatgtgacaagcagggtttccccatgaagCAGGGTGTCTTGACCCAGGGACGTGTGCAACTGCTGATGCACCGAG

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ14726 (Selaginella moellendorffii), 3'ss of exon 2
gtaatttctttggcaatttgctccatga-ttcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
                         ||| ||| ||  |  |   ||| |    |  |||      ||||| ||  | |    | ||||||||||| |||||||| ||||||||||||||||| ||||||||| | || ||||| ||||||||||| || || |   |    ||||| ||||| ||  
------------------------gtgaattcgtcggcatttgagctttgctgtttgtt------ctaagatttgcag----tgcagGAATTCAAAGGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTCCTCAAGACGAAGCGTGTGCGCCTCCTGT

upper sequence: LOC_Os03g27260.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ26393 (Selaginella moellendorffii), 3'ss of exon 2
gtaatttctttggcaatttgctccatga-ttcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
                         ||| ||| ||  |  |   ||| |    |  |||      ||||| ||  | |    | ||||||||||| |||||||| ||||||||||||||||| ||||||||| | || ||||| ||||||||||| || || |   |    ||||| ||||| ||  
------------------------gtgaattcgtcggcatttgagctttgctgtttgtt------ctaagatttgcag----tgcagGAATTCAAAGGCTATGTCTTCAAGATCATGGGAGGATGTGACAAGGATGGCTTCCCTATGAAGCAGGGCGTTCTCAAGACGAAGCGTGTGCGCCTCCTGT

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|313079530|gb|HO213088.1|HO213088
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|4881015|gb|AU065314.1|AU065314
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|88355433|gb|CI679149.1|CI679149
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GGATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|6449568|gb|AU081510.1|AU081510
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTNACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|3763665|gb|AU030417.1|AU030417
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|88302324|gb|CI668170.1|CI668170
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|4880957|gb|AU065256.1|AU065256
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|4880899|gb|AU065198.1|AU065198
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|33657451|gb|CF280065.1|CF280065
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAT                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|33654579|gb|CF277193.1|CF277193
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|88428463|gb|CI564931.1|CI564931
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|58683420|gb|CK072107.1|CK072107
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|88726151|gb|CI749806.1|CI749806
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|33676302|gb|CF304541.1|CF304541
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|33654394|gb|CF277008.1|CF277008
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|88581386|gb|CI698367.1|CI698367
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GGATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|25800692|gb|CA756653.1|CA756653
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
EST: gi|33663296|gb|CF294263.1|CF294263
EST:     TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAA                         GAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT
genomic: TTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGT

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: 75 (upstream exon), 58 (downstream exon)
Score: 174

CCGGGCATTTTATGACAAGAGGATCTCCCAGGAAGTCAGTGGTGATGCTCTTGGCGAAgtaatttctt ... gtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC
               atttaat  putative branch site (score: 174)
                                          tctgttt  putative PPT
              tatttaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttctttggcaatttgctccatgattcttcaactgtcttgctatttaatgagttggatgactaagtttgtctgtttgtacagGAATTCAAGGGCTATGTATTCAAGATCATGGGAGGCTGTGACAAGCAAGGTTTCCCCATGAAGCAGGGTGTGCTTACTTCTGGACGTGTCCGCCTTCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC