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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTCATCTCCGTTTGAGGGATCCTACAGTACCGGAGAGAGTAAATCTTCCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaattggcctttcttacttgaatgaaagataacctacaattaagtactgaatgcccaaacaaggattgctaatcacttctgccatacatgttctcatgcag

Basic information

species Oryza sativa
transcript LOC_Os10g37210.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37210.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G032222_T03 (Zea mays), 5'ss of exon 16
CTCCTCATCTCCGTTTGAGGGATCCTACAGTACCGGAGAGAGTAAATCTTCCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaattggcctttcttacttgaatgaaagataa--cctaca---attaagtactgaatgcccaaac-----aaggattgctaatcacttctgccatacatgttctcatgcag
| ||||||||||| |||||||||||||||||||| ||  |||||||| || | |||||||| |  ||||| ||||  ||||| ||||| || ||||||||||| | ||| | |||  || |  ||||||    | |    ||| ||   || ||  ||| || ||   |       |  | || || |||||| |||   |   |||| ||||| ||
CGCCTCATCTCCGCTTGAGGGATCCTACAGTACCCGAACGAGTAAATGTTGCACTGTATGCAGCGCCAGAATCACGCTATTGCCCAGCCCGGGTTTACGAgtacgtaaactagccactccttgttgaattcccgttgctcccttcatgcatcaatgactcaaagctttagtggccaagagttttctgatcactactg---tgtctgttttcatgtag
















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|88245808|gb|CI245657.1|CI245657
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29615151|gb|CB620164.1|CB620164
EST:     CCTCTGTATGCTGGACCAGAGTCACGTTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88280721|gb|CI401919.1|CI401919
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88273475|gb|CI393881.1|CI393881
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCAAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88259171|gb|CI363464.1|CI363464
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29657656|gb|CB653931.1|CB653931
EST:     CCTCTGTATGTTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29675569|gb|CB671844.1|CB671844
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29662394|gb|CB658669.1|CB658669
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACTGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|86889572|gb|CI318763.1|CI318763
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATNTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29637767|gb|CB642776.1|CB642776
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|86859459|gb|CI278866.1|CI278866
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88279088|gb|CI400088.1|CI400088
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88278566|gb|CI399566.1|CI399566
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTTTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAGA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88280463|gb|CI401661.1|CI401661
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29669361|gb|CB665636.1|CB665636
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88489550|gb|CI426822.1|CI426822
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29667105|gb|CB663380.1|CB663380
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29676401|gb|CB672676.1|CB672676
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29659147|gb|CB655422.1|CB655422
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|29681493|gb|CB677768.1|CB677768
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
EST: gi|88291777|gb|CI539948.1|CI539948
EST:     CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGA                         GTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA
genomic: CCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAA

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: 65 (upstream exon), 53 (downstream exon)
Score: 10

CTCCTCATCTCCGTTTGAGGGATCCTACAGTACCGGAGAGAGTAAATCTTCCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaat ... tctcatgcagGTATGTCACCGACGAGAAAGGTGACCAGAAGCTTCACATAAATGCTCAAAATTGTCTTCATTGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTCATCTCCGTTTGAGGGATCCTACAGTACCGGAGAGAGTAAATCTTCCTCTGTATGCTGGACCAGAGTCACATTATTGTCCAGCTCGAGTTTACGAgtaaggaaattggcctttcttacttgaatgaaagataacctacaattaagtactgaatgcccaaacaaggattgctaatcacttctgccatacatgttctcatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC