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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGATGCGGGATTCAAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctggatgtgtatgcatgatatttaggttgctatgtttcacagataataatgtcttgctttaatgtctccctacag

Basic information

species Oryza sativa
transcript LOC_Os09g02700.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g02700.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G102829_T02 (Zea mays), 5'ss of exon 4
GTGATGCGGGATTCAAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctg----gatgtgtatgcatgatatttaggttgctatgtttcacagataa--taa-tgtcttgctttaatgtctccc-tacag
|| ||||||||||| |||||||||||||||||||||||||||||||| || ||||||||||||||||||  |||||||||| ||||    |   ||| |  |  |    |   ||| | ||    ||| ||||  ||| | ||||   || || |||||| |  ||
GTTATGCGGGATTCGAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCTTTCAAATCTGCTGAAGATGCTAACCGAGCTgtatgctgttttgtcatgtgtttagtaatactgatttgatttggcaaacacataaaataactttcttatcttgatttctcccatgtag
















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|300215682|gb|HO088308.1|HO088308
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|33678932|gb|CF307171.1|CF307171
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|33794298|gb|CF323036.1|CF323036
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|29682165|gb|CB678440.1|CB678440
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCCAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|38478300|gb|CF962433.1|CF962433
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|38475210|gb|CF959343.1|CF959343
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|25797580|gb|CA753541.1|CA753541
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|218478348|gb|FG964722.1|FG964722
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|58660405|gb|CK049085.1|CK049085
EST:     GGTTCTGGATTTGTTGCG-TTAAGAGTCGGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GGTTCTGGATTTGTTGCGTTTAA-A-TCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|87024520|gb|CI290050.1|CI290050
EST:     AGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: AGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|33795349|gb|CF323545.1|CF323545
EST:     GTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|9788904|gb|BE530914.1|BE530914
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|29639372|gb|CB644381.1|CB644381
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|33678877|gb|CF307116.1|CF307116
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|29677178|gb|CB673453.1|CB673453
EST:     TAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCTAGATGGTTGGCAGCAAAACGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|286590|gb|D15397.1|D15397
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|218479615|gb|FG956762.1|FG956762
EST:     GCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|2310956|gb|C27111.1|C27111
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|86830802|gb|CI293786.1|CI293786
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATTTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|218493366|gb|FG968669.1|FG968669
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|218481961|gb|FG961969.1|FG961969
EST:     GAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|55828027|gb|AU065739.2|AU065739
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|58591029|gb|CF989337.1|CF989337
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|218500549|gb|FG964038.1|FG964038
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
EST: gi|29645073|gb|CB650080.1|CB650080
EST:     GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCT                         CTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG
genomic: GAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCG

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), 74 (downstream exon)
Score: 178

GTGATGCGGGATTCAAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctgga ... ctccctacagCTTGCCGAAATGAACAGCAAGATGGTTGGCAGCAAACCGCTCTACGTTGCGCTTGCACAGCGCAAGGAAGACAGGAAAGCAAGGCTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGATGCGGGATTCAAATGGTGTCAGCAGAGGTTCTGGATTTGTTGCGTTTAAATCTGCTGAAGATGCTTCCCGAGCTgtaagctggatgtgtatgcatgatatttaggttgctatgtttcacagataataatgtcttgctttaatgtctccctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG