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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag

Basic information

species Oryza sativa
transcript LOC_Os02g52920.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G414569_T01 (Zea mays), 5'ss of exon 2
TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgc-tgacggtccatatgaccatatttcactgatgtccagtttaat--tcactgcttctctaattgctgcaatctaattccttttgtag
||| ||||||||||| |||||| ||||| | |||||||| ||||||||||| || ||| |||| |||||||||| ||| ||||||||||||||||||||||| ||  |  |  | ||   || |    || || |   | |   |  |   || | || || |  |||  |   || || |  | |   | |   ||  |   || || ||
TAGTGCAGAGAAAGGATCAGGAGTATCTGTGAATCTTGACTGGAAGATTGGGATCGCAACAAAAGATTGGGATGCTATTGCTAAGAAGGAAAAAATTGAGgtcgggatgcgaattgctgtaccgagctacagttc---taaatgtcatgagctcaagttcaatgcaatatttggtgtttgttaattgaataccgcctc-tcttttgtgcag

upper sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G19840.1 (Glycine max), 5'ss of exon 3
TAGCGCAGAGAAAGGGTCAGGAATATC--TATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag
   |  |  ||| | |   |  |  |   | | || ||||||||||| | |||||||||||| ||||||||||||    | ||||| ||||| || |||||||||    |    || |   |  |     |  |  ||||| |   ||   | |    || ||   ||||   || ||||        |   | |       |    |  
--TCATAATGAACGAGGTGGAGACGTTAGTGTGAACCTTGATTGGAAAACTGGAATTGCAGCCAAGGATTGGGATTCGGTTGCTAAAAAGGAGAAGATTGAGgtaaatatttcattggt--atttataatctattaatatgcctg-ataataatttcatctag---aattttttggttctacgtcacatctgaccaggactataacat--

upper sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA05G30330.1 (Glycine max), 5'ss of exon 2
-TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag
  |  |   || |   ||   |  ||  | | || ||||||||||| |||||||||||||| ||||||||||||    | ||||  || || || |||||||||    |   |  ||  | ||   | |   |  || |  | | | |  |   |  |  |  |||| |   |    |   ||  ||||  || || |     |     
CCATAGTCAAGGAGTTGTTGAGGTTAA-TGTAAACCTTGATTGGAAAATTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAGAAAAGAGAAGATTGAGgtaaactt---ccaagagatacgcataattttgaatctccctacactataggtagatagaacttaagtgttttacccatcaagggctgacatttactctaggt-----

upper sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA15G05190.1 (Glycine max), 5'ss of exon 2
TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaa-actgctga-cggtccatatgacc-atattt-cactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag
||| | |      ||   ||   |   | | || ||||||||||| | |||||||||||| ||||||||||||    | ||||| || ||||| |||||||||     |   || | |   | |  | | |  |  ||||| |  || ||| ||   |       |||| |||  | | || | ||  |||| |  |||   |         
TAGTGAACGAGCTGGTGGAGACGTTAGTGTGAACCTTGATTGGAAAACTGGAATTGCAGCCAAGGATTGGGATTCAGTTGCTAAAAAAGAAAAGATTGAGgtaattaaacatttcgtcggtattattaatctattgatatgcctgatgttttcatctagaatttttttagttc--tacctcacaaaa-gctgtatactataac---------

upper sequence: LOC_Os02g52920.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G13470.1 (Glycine max), 5'ss of exon 2
TAGCGCAGAGAAAGGGTCAGGAATATC--TATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag
   |  ||  || | ||  |  |  |   | | || ||||||||||| |||||||||||||| |||||||||||| | |  ||||  || || || |||||||||    |   |  ||  | |    | |   |  || |  | ||| |  |   |  |  |  |||| |   |        ||  ||||  || |  |     |     
-GCCCTAGTCAAGGAGTTGGTGAGGTTAATGTAAACCTTGATTGGAAAATTGGAATTGCAGCTAAGGATTGGGAT-TCAGTGCTAGAAAAGAGAAGATTGAGgtaaactt---ccaagagatatgtataattttgaatctccctatactataggtagatagaacttaagtgttttacctatcaagggctgacatttgctcaaggt-----

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|88843250|gb|CI372150.1|CI372150
EST:     GGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|66920229|gb|CX107077.1|CX107077
EST:     GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|88206325|gb|CI206174.1|CI206174
EST:     GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|11026623|gb|AU163224.1|AU163224
EST:     AATTGCAGCAAAGGATTGGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATNCATCCAT
genomic: AATTGCAGCAAAGGATTGGG-ATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|163925933|gb|EG709657.1|EG709657
EST:     GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|2428877|gb|C73340.1|C73340
EST:     GCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|89184446|gb|CI047011.1|CI047011
EST:     GATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|218497308|gb|FG954388.1|FG954388
EST:     GAATTGCAGCAAAGGATTGGGATGATATCGCTAAGAAGGACAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|87013522|gb|CI267223.1|CI267223
EST:     GAATTGCAGCAAAGGATTGGGATGTAATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|29682187|gb|CB678462.1|CB678462
EST:     GAATTGCAGCAAAGGATTGCGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAAAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|88843865|gb|CI011123.1|CI011123
EST:     GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
EST: gi|88982839|gb|CI028252.1|CI028252
EST:     GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAG                         GGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT
genomic: GAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCAT

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: 72 (upstream exon), 71 (downstream exon)
Score: 18

TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtag ... ccttttgtagGGTGTAGAACTAGAGCTTAGAAAACTTGAAGTGGCAGTACAATCCATCCATCAGAACATGATATATCTCAAAGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCGCAGAGAAAGGGTCAGGAATATCTATTAATCTTGATTGGAAGATTGGAATTGCAGCAAAGGATTGGGATGTTATCGCTAAGAAGGAAAAAATTGAGgtaggagtaggcttagccaaactgctgacggtccatatgaccatatttcactgatgtccagtttaattcactgcttctctaattgctgcaatctaattccttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA