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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGCCTCACCAAGTTCCCCAGCCTTCCTCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaattggatgtttgcttttatattaatttctgcctaaaatgtgctacacttgttacatttgattgattctgtacatggttagttactcttgaa...

Basic information

species Oryza sativa
transcript LOC_Os07g25420.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g25420.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G073077_T01 (Zea mays), 5'ss of exon 2
GTCCGCCTCACCAAGTTCCCCAGCCTTCCTCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa-ttggatgtt-tgcttttatattaatttctgcctaaaatgtgctacacttgttacatttgattgattctgtacatggttagttactcttgaa
||||  |||||||| |||||||||||||| || |||||| |||||||||| || || ||||| ||||| ||| |||| ||||||||    ||||   |  || |||| ||||| ||  ||||  |      |   |  || |  | |  ||  |   | |   |  ||  ||| || |   
GTCCATCTCACCAAATTCCCCAGCCTTCCGCCCTCATTTGAGCAGACACCTAAAGCCGTGGAGGAGCTCAAACTTGCAAgtaagatggccttgggcctcatggttttttattagttgatgccatagcgaccccctaagtgctctagtatatgcaaaat-tgggttcttgattattcgtat-
















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|88688587|gb|CI732163.1|CI732163
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|8856245|gb|AU093563.1|AU093563
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88412237|gb|CI573513.1|CI573513
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|33819689|gb|CF335663.1|CF335663
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88309199|gb|CI655207.1|CI655207
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAACACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|33658971|gb|CF281584.1|CF281584
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88333830|gb|CI643862.1|CI643862
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88424460|gb|CI608046.1|CI608046
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88328055|gb|CI649853.1|CI649853
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|58681161|gb|CK069848.1|CK069848
EST:     TCCATCATTTCAGCAGACACCGAATGCAGGGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88364221|gb|CI612170.1|CI612170
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGGAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88345880|gb|CI632353.1|CI632353
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGGGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88358913|gb|CI619417.1|CI619417
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGGGA                         GGGAAATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88737020|gb|CI760528.1|CI760528
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88348768|gb|CI631462.1|CI631462
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|2427780|gb|C72243.1|C72243
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88737992|gb|CI761500.1|CI761500
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88395474|gb|CI612996.1|CI612996
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88377414|gb|CI602899.1|CI602899
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88391840|gb|CI603359.1|CI603359
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88726404|gb|CI750059.1|CI750059
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|33654136|gb|CF276750.1|CF276750
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88745467|gb|CI768827.1|CI768827
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88305511|gb|CI630673.1|CI630673
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|218496609|gb|FG945909.1|FG945909
EST:     TCCATCGTTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88393359|gb|CI618247.1|CI618247
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88305623|gb|CI631990.1|CI631990
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGCTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|58586987|gb|CF985295.1|CF985295
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCGGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88723691|gb|CI747201.1|CI747201
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88744040|gb|CI767400.1|CI767400
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88392419|gb|CI612893.1|CI612893
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCACGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|218495940|gb|FG948496.1|FG948496
EST:     TCCATCGTTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|218498577|gb|FG966054.1|FG966054
EST:     TCCATCGTTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88326392|gb|CI659822.1|CI659822
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|88383951|gb|CI631841.1|CI631841
EST:     TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: TCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
EST: gi|2443022|gb|C74793.1|C74793
EST:     GAGCTGAAAATTGCGA                         GGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG
genomic: GAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAG

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), 74 (downstream exon)
Score: 93

GTCCGCCTCACCAAGTTCCCCAGCCTTCCTCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaa ... aatctttcagGGGACATCTATGAGCATGCAGTTGTTCTGAGTGTGAAAATTGAAGACCAAGATGCATTTGAAAGGGACTTTTGTCAACTCAAACCTTATTACATGGATAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGCCTCACCAAGTTCCCCAGCCTTCCTCCATCATTTCAGCAGACACCGAATGCAGTGGAAGAGCTGAAAATTGCGAgtaagattaattggatgtttgcttttatattaatttctgcctaaaatgtgctacacttgttacatttgattgattctgtacatggttagttactcttgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA