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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtgttcttttattttgaaagatggcatactactgattactaaccttcaacatctctggtttcag

Basic information

species Oryza sativa
transcript LOC_Os01g62900.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62900.1 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G028535_T01 (Zea mays), 5'ss of exon 20
CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtgttctttta----ttttgaaagatggcatactact----------gattactaacct-tcaacatctctggtttcag
|||||| || || ||||||||||| ||||| || ||||||||||| ||||||||||||| ||| || |||||||| ||||| | ||| |  |  || |    | |||||| |     || |  |          | ||| |||| | ||    |   | ||| |||
CATTTTGCGCGGTAGTGGACAAGTGGTGAATGGTGACAAGGGAGTGGTTTACACCCACAAGGATCTTCCTTTGCAATGAGgcaagtaataatagttcacacttgttgaaaaagaatttattttttttctacgacggttattaacttatctctgttctttgttgcag
















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|88462433|gb|CI514565.1|CI514565
EST:     AGGGATTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: AGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88254967|gb|CI353791.1|CI353791
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|428854|gb|D25010.1|D25010
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTNAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|87028718|gb|CI349437.1|CI349437
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88436007|gb|CI516543.1|CI516543
EST:     CTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88690367|gb|CI734446.1|CI734446
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTACAGCAATTTTTTGCAGACGCCC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|44670561|gb|CR283995.1|CR283995
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|38471160|gb|CF955291.1|CF955291
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88691820|gb|CI733397.1|CI733397
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88265249|gb|CI369023.1|CI369023
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88690168|gb|CI734247.1|CI734247
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88273346|gb|CI388802.1|CI388802
EST:     CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|33683777|gb|CF312016.1|CF312016
EST:     GGCGACAAGGGAGTTGTTTACACCCCACAGGGAGCTCCCTTTGCAGTGAG                         GTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: GGCGACAAGGGAGTTGTTTACA-CCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
EST: gi|88261597|gb|CI365173.1|CI365173
EST:     CGCCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAG                         -TGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC
genomic: CGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTC

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: 70 (upstream exon), 55 (downstream exon)
Score: 6

CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtg ... ctggtttcagGTGAAGTGGCTTGTGAAGGAGCTGTTGTAGAGCAATTTTTTGCAGACGCTCACCGTGCTCCTCCTTGAGAGCTGCTTCTCTTCATGACATGCAATGGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTTACGAGGAAGTGGACAAGTAGTGAACGGCGACAAGGGAGTTGTTTACACCCACAGGGAGCTCCCTTTGCAGTGAGgtaggtagtgttcttttattttgaaagatggcatactactgattactaaccttcaacatctctggtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT