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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctcagcaacctctacaaacaattgttgttacccaacctgtttcgtgatgtgcaactgatcatcctgttttactgtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACAGGACGGTTACCCTGCGTGATTCGTATGGGAAAGCTGGGCCAAAGTGATT

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G032049_T01 (Zea mays), 3'ss of exon 21
gtaatctcagca------acctctacaaacaattgttgttacccaacctgtttcgtgatgtgcaactgatcatcctgttttactgta-attccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACAGGACGGTTACCCTGCGTGATTCGTATGGGAAAGCTGGGCCAAAGTGATT
||||| |||| | ||| | | | | || | ||| |||| | | ||||| || |||| ||| ||| |||| ||| |||||||| ||||| || ||||| ||||||||||| | ||||||||||| || |||||||| |||||||||| ||||||||||| || |||||| |
gtaatttcagagctagagaattctctatatatt--acgtcattcaatgggttttcacaact-caactaattgtcctactttgatgtggattctagGTTACTTCGCCGTGGATACTGACTCCACACCTGAGAAACTCGTGTTCAACAGAACTGTTACCCTCCGTGATTCGTTCGGGAAAGCTGGACCCAAGTGACT

upper sequence: LOC_Os01g09000.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G048012_T01 (Zea mays), 3'ss of exon 20
gtaatctcagcaacctctacaaacaattgttgt-tacccaacctgtttcgtgat----gtgcaactgatcatcctgttttactgta-attccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACAGGACGGTTACCCTGCGTGATTCGTATGGGAAAGCTGGGCCAAAGTGATT
||||| |||| | || | || ||| || || | | | | || | |||||||| || || ||| ||| |||| ||| |||||||| |||||||| ||||| || |||||||| | ||||||||||| || || ||||| |||||||| | || |||||||| ||||||||| |
gtaatttcag--agctagagaacttcctgtggtacacgccattcgatgggttttcacaactcaactgattgtcttgctttgatgtggattctagGTTACTTCGCCGTGGACACGGACTCCACTCCTGAGAAGCTCGTGTTCAACAGAACTGTCACCCTCCGTGATTCATTCGGTAAAGCTGGACCAAAGTGACT
















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|86431241|gb|CI083664.1|CI083664
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88197986|gb|CI197836.1|CI197836
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|86430461|gb|CI082884.1|CI082884
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|29673631|gb|CB669906.1|CB669906
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|86495415|gb|CI138048.1|CI138048
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|87017890|gb|CI273912.1|CI273912
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAAAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88480768|gb|CI418039.1|CI418039
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|86895282|gb|CI331220.1|CI331220
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCCCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|86478328|gb|CI120961.1|CI120961
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88232271|gb|CI230729.1|CI230729
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|29660828|gb|CB657103.1|CB657103
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|87030255|gb|CI270265.1|CI270265
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88967128|gb|CI392090.1|CI392090
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|86482312|gb|CI124945.1|CI124945
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88197825|gb|CI197675.1|CI197675
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88273491|gb|CI393897.1|CI393897
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|87041341|gb|CI195963.1|CI195963
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88451099|gb|CI534092.1|CI534092
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|86597706|gb|CI274697.1|CI274697
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACGAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
EST: gi|88966267|gb|CI119402.1|CI119402
EST:     ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAG                         GCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA
genomic: ATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACA

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: 48 (upstream exon), 75 (downstream exon)
Score: 17

GATCTTAACCCGAACTCAAAAGAGGTGATCAAGGGTGCCTACGCCGTGCCATCGCTTGCGACTGCGGTTCTTGGTGACAAGTTCCAGTTCGAGCGGCTAGgtaatctcag ... gtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACAGGACGGTTACCCTGCGTGATTCGTATGGGAAAGCTGGGCCAAAGTGATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacccaacctgtttcgtgatgtgcaactgatcatcctgttttactgtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACAGGACGGTTACCCTGCGTGATTCGTATGGGAAAGCTGGGCCAAAGTGATT
                        aactgat  putative branch site (score: 17)
 tgtttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctcagcaacctctacaaacaattgttgttacccaacctgtttcgtgatgtgcaactgatcatcctgttttactgtaattccagGCTACTTCGCAGTGGACACAGACTCGACACCTGAGAACATTGTGTTCAACAGGACGGTTACCCTGCGTGATTCGTATGGGAAAGCTGGGCCAAAGTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG