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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCAAATTCTGCTTCCATGAGAACTTAGTTCTGCTTGCAGATGAAGTCTATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttgatttctgacccgtgatgctttatcatgaatacaacatttcccaaccttttactttcatgtggtataccaaaaattaaaatgaacataata...

Basic information

species Oryza sativa
transcript LOC_Os07g01760.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 7
TCTCAAATTCTGCTTCCATGAGAACTTAGTTCTGCTTGCAGATGAAGTCTATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttgatttctgacccgtgatgcttt-atcatgaatacaacatttc---ccaaccttttactttcatgtggtat-accaaaaattaaaatgaacataata------
| |   ||  |||| |||||| |||||||||||||||||||| ||||| ||||| |||||| |||||||||||||||||||||||||||| || ||||||||| ||||||||||||| ||  | || ||||  |||||||  ||   || |      ||||     |   || |||  | |||||||  |    |   |    |       
TGTGCGATATTGCTACCATGAAAACTTAGTTCTGCTTGCAGACGAAGTGTATCAGCAGAACGTTTATCAAGATGAGCGCCCATTTATAAGCGCAAGAAAGgta-cttttgatttctggccaataattcttttgtcatgaactcatggttgcaacttgacctaggcttaatatttgggctcaccaaaacatgcctttctcgactttttccag

upper sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv00s0225g00130.t01 (Vitis vinifera), 5'ss of exon 8
TCTCAAATTCTGCTTCCATGAGAACTTAGTTCTGCTTGCAGATGAAGTCTATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgta-acttttgatttctgacccgtgatgcttta-tcatgaatacaacatt-tcccaaccttttactttcatgtggtataccaaaaattaaaatgaacataata
  |  | ||||| | ||| || ||||||||  |||||| ||||||||| || |||||||| ||||| || ||||||||||| ||||| |||||||||||||||      || | |   |      || | |   || | |     | | | ||   |  || |||   ||| |  |   ||||   | |||            
ATTGCACTTCTGTTACCAAGAAAACTTAGTCTTGCTTGGAGATGAAGTTTACCAACAGAATATTTACCAGGATGAGCGCCCTTTTATCAGTGCTAGAAAGgtatggcgctgttatgaaattaactattcctgggtctttacctggagactatcttgaatttatac---catattttcctccaaccctgaaag-----------
















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|29615657|gb|CB620669.1|CB620669
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|29671704|gb|CB667979.1|CB667979
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|58611970|gb|CK039682.1|CK039682
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGCAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33799763|gb|CF325747.1|CF325747
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33381539|gb|CF196882.1|CF196882
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|29684690|gb|CB680965.1|CB680965
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GATCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33381769|gb|CF197112.1|CF197112
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATAGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|29645692|gb|CB650699.1|CB650699
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|58688608|gb|CK077295.1|CK077295
EST:     TCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGAGAGTGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTC
genomic: TCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACA-TGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTC
EST: gi|33381143|gb|CF196486.1|CF196486
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGNAAG                         GTTCTGTTTGACATGGGTCCTCCTATGNNNANNGANNTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|13420573|gb|AU174663.1|AU174663
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|29615822|gb|CB620834.1|CB620834
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33381689|gb|CF197032.1|CF197032
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTNNNNNN                         NTTCTGTTTGACATGGGTCCTCCTA
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTA
EST: gi|33381622|gb|CF196965.1|CF196965
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33665284|gb|CF296251.1|CF296251
EST:     CATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: CATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33801487|gb|CF326616.1|CF326616
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|88357956|gb|CI650692.1|CI650692
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|58588206|gb|CF986514.1|CF986514
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33381833|gb|CF197176.1|CF197176
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|33675257|gb|CF303496.1|CF303496
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|5667553|gb|AU077813.1|AU077813
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|88342691|gb|CI657185.1|CI657185
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTACAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|701822|gb|D48113.1|D48113
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|11442608|gb|BF430511.1|BF430511
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|29689279|gb|CB685554.1|CB685554
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
EST: gi|38479882|gb|CF963971.1|CF963971
EST:     ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAG                         GTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT
genomic: ATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCT

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), 72 (downstream exon)
Score: 239

TCTCAAATTCTGCTTCCATGAGAACTTAGTTCTGCTTGCAGATGAAGTCTATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttg ... atttcttcagGTTCTGTTTGACATGGGTCCTCCTATGAGCAGGGAAGTTCAGCTGGTTTCTTTCCATACTGTGTCAAAAGGATATTGGGGGGAGTGTGGACAACGTGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCAAATTCTGCTTCCATGAGAACTTAGTTCTGCTTGCAGATGAAGTCTATCAACAGAACATTTATCAAGATGAGCGCCCATTTATAAGTGCTAGAAAGgtaacttttgatttctgacccgtgatgctttatcatgaatacaacatttcccaaccttttactttcatgtggtataccaaaaattaaaatgaacataata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccaacc