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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTTTTACCATATATCATTTCTTCCTTTGGTCCTGACAAATCAGTTGCTGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgcttttaagctaaggcgtcaagagaatgttgttatatttatgcacaagtgccaacagtgtttctatattgagaccgttttataaattcagtttagtactgactagttgcacgtgtatccttttcattgttgtctgcag

Basic information

species Oryza sativa
transcript LOC_Os06g39344.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39344.3 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G047564_T02 (Zea mays), 5'ss of exon 7
AAGTTTTTACCATATATCATTTCTTCCTTTGGTCCTGACAAATCAGTTGCTGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgcttttaagc---------taaggcgtcaagagaatgttgttatatt---tatgcacaagtgccaac------agtgtttctatattgagaccgttttata----aattcagtttagtactgact-----------------agttgcacgtgtatccttttcattgttgtctgcag
||| |||| ||||||||||||||||| ||  ||||||| |||||||| |||||||||||||||||||| ||||| ||||| | ||||| ||||||||||||||| | ||| | || |         ||  ||  |  |  ||   |  | ||||    |    ||| ||   ||      |    | |  || |      ||  |||     |||| | |  | || || ||                 | || |||   || |  || |  || || ||||||
AAGCTTTTGCCATATATCATTTCTTCTTTCAGTCCTGATAAATCAGTGGCTGAATCTGTGGAAGAGCTAAAGAAATGTAGCCGAAGTGGTGATGCTGCAGgtaccc-gctatgaaacattcccttttagtgcaccttggcaacactaatgtattactcacatgcaactgttgacttttaaaaaactcccctactttctttgtgctatgtaagaatttaatgcaatagtggcttaagaagggataactgcatttacacacttaactgttcctctggtggctgcag
















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|29664860|gb|CB661135.1|CB661135
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|33814601|gb|CF333165.1|CF333165
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGNGCCTTGGCAGGACTCAAAAAAGGGGCTCCA
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAG-GCCTTGGCAGGACTCAAAAAAGGGGCTCCA
EST: gi|24468726|gb|CA305675.1|CA305675
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|86876099|gb|CI325595.1|CI325595
EST:     AAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: AAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|29658500|gb|CB654775.1|CB654775
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|29614417|gb|CB619430.1|CB619430
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|86874376|gb|CI316742.1|CI316742
EST:     GGAAGAGC-TAAAAAGGGTAGTCAAAGTGATTATGCTGCAG                         TTGCAGAATGGGCCAACGAGGGCCTTGGCAGGACTCAAAAAAGGGGCTCCA
genomic: GGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGA-GGCCTTGGCAGGACTCAAAAAAGGGGCTCCA
EST: gi|33813303|gb|CF332538.1|CF332538
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCTCTTGGCAGGACTCAAAAAAGGGGCTCCA
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGC-CTTGGCAGGACTCAAAAAAGGGGCTCCA
EST: gi|86418684|gb|CI053485.1|CI053485
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|86859810|gb|CI345448.1|CI345448
EST:     GAGCTTAAGAAGTGTAGTCAAAGTGATCATGCTGCAG                         TGGCACAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAA-GGGCTCCAT
genomic: GAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|38475804|gb|CF959937.1|CF959937
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|33653651|gb|CF276265.1|CF276265
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|86497764|gb|CI140397.1|CI140397
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|702653|gb|D48944.1|D48944
EST:     TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: TGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|88265173|gb|CI368947.1|CI368947
EST:     AAGTGATGATGCTGCAG                         TGGCAGAAT-GGCCAAC-AGGCC-TGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: AAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
EST: gi|86835525|gb|CI347982.1|CI347982
EST:     GTCAAAGTGATGATGCTGCAG                         TGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT
genomic: GTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCAT

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: 74 (upstream exon), 47 (downstream exon)
Score: 48

AAGTTTTTACCATATATCATTTCTTCCTTTGGTCCTGACAAATCAGTTGCTGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgct ... ttgtctgcagTGGCAGAATGGGCCAACGAGGCCTTGGCAGGACTCAAAAAAGGGGCTCCATTTTCTCTATGTTTAACTCAAAAACATTTTTCTCAAGTTGCATCAGCATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTTTTTACCATATATCATTTCTTCCTTTGGTCCTGACAAATCAGTTGCTGAATCTGTGGAAGAGCTTAAGAAGTGTAGTCAAAGTGATGATGCTGCAGgtactctgcttttaagctaaggcgtcaagagaatgttgttatatttatgcacaagtgccaacagtgtttctatattgagaccgttttataaattcagtttagtactgactagttgcacgtgtatccttttcattgttgtctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG