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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataggcctgatttgctacttcattgtcaatgatactaagccaattcgtatatgtgaaaaatataatatgttgtgtgtatcttccatcacttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCT

Basic information

species Oryza sativa
transcript LOC_Os03g60740.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g60740.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G068244_T01 (Zea mays), 3'ss of exon 5
aataggcctgatttgctacttcattgtcaatgatactaagccaattcgtata--tgtgaaaaatataatatgttgtgtgtatcttccatcacttccatgt-agGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCT
  | |   |    ||   ||  | |   || || | |   | | || || |   | |       ||||| || ||    | |||||  |  |||  || | ||||| || ||||| |||||||| ||||| |||||||| ||| |  |||| || || |||||||||||||||||||| ||||| ||||| ||||| ||||| 
-ctggaaatcgcatgaggct--aatacaaaagaaaatctccaattttgtttccttctctgttgcataatctgatgctgttttcttctgtgccttaaattttagGCCAGGAGGTCTACAAGACAAGGACGGAGGAGTGAGAGAGCTACTTGTGGGGAAAGACGATGAACTTCTCCAGACTGACACAAAGTCGATTCCTAGAGCC
















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|109711615|gb|CI013220.1|CI013220
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|33818134|gb|CF334893.1|CF334893
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|3762111|gb|C99359.1|C99359
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|33686688|gb|CF314927.1|CF314927
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         CCCTGGTGGTCTGCAAGACAAAG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAG
EST: gi|32947908|gb|BP184480.1|BP184480
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGG-AGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|88490376|gb|CI427648.1|CI427648
EST:     GTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: GTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|163923266|gb|EG711075.1|EG711075
EST:     AAGTCACAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|89189979|gb|CI013546.1|CI013546
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|33821839|gb|CF336730.1|CF336730
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|3762112|gb|C99360.1|C99360
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|88847804|gb|CI005990.1|CI005990
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|89198494|gb|CI007554.1|CI007554
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|33817947|gb|CF334802.1|CF334802
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|117234788|gb|CT847886.1|CT847886
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGATGGCCTGCAAGACAAAGACGGGGGAGTGAGGGAGGTTGATTGTTG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAG-TTGATTGTTG
EST: gi|86537041|gb|CI177247.1|CI177247
EST:     CCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: CCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|88239537|gb|CI240014.1|CI240014
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|86506649|gb|CI149282.1|CI149282
EST:     CCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: CCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|33660166|gb|CF291133.1|CF291133
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|86507076|gb|CI149709.1|CI149709
EST:     ATACTATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: ATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|88227808|gb|CI227288.1|CI227288
EST:     AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: AAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|55415365|gb|CV727741.1|CV727741
EST:     TTATACAATAATAAG                         GCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
genomic: TTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGG
EST: gi|42592251|gb|CK738737.1|CK738737
EST:     AGTCAGAACAGTATTTGGGCAAACGGTGGAGTCCCTTATACAATAATAAG                         GCCCTGGTGGCCTGCAAGACAAAGAC
genomic: AGTCAGAACAGTATTTGG-CAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCC-TGGTGGTCTGCAAGACAAAGAC

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: 37 (upstream exon), 75 (downstream exon)
Score: 115

GTTTGGAAGCGCAAGTCAGAACAGTATTTGGCAGACAGTGGAGTCCCTTATACAATAATAAGgtaccacctg ... ttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtatatgtgaaaaatataatatgttgtgtgtatcttccatcacttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCT
                                  tcttccatcacttcc  CT-rich tract
     tatgtgaaaaatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataggcctgatttgctacttcattgtcaatgatactaagccaattcgtatatgtgaaaaatataatatgttgtgtgtatcttccatcacttccatgtagGCCTGGTGGTCTGCAAGACAAAGACGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- -aggcctg
- - - - - - -tgctact
- - - - - - - - - - - - - - - tgatact
- - - - - - - - - - - - - - - - - - -aagccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt