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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcacatcttacctttcaacatttcactggttgcaataaatttttctttcagagatacttctctgaagcttctgaactatgtttctcccaaccttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT

Basic information

species Oryza sativa
transcript LOC_Os09g24320.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G121200_T01 (Zea mays), 3'ss of exon 5
----------------agcacatcttacctttcaacatt--tcactggttgcaataaatttttctttcagagatacttctctgaagcttctgaactatgtttctcccaaccttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT
| | | || | | | || | | |||| |||||| | | ||||||| || | | ||| | ||||| ||||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| ||||||||||||| |||| ||||
ctcacagaacaggggcaaaaaaaaaccccccacgatcctggtccataatagcaaccaattttccctgcagagatggtt-------gatcctgccatttgttt-----------ttcagGTGAATGTTACTGCTGATCACAGGATTATCTATGGTGCTGATTTGGCAGCATTCCTGCAAACATTTGCAAAGATTGTTGAGGATCCTGAATGCCTCACAT

upper sequence: LOC_Os09g24320.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g03380.t01 (Vitis vinifera), 3'ss of exon 5
agcacatcttacctttcaacatttcactggttgcaata--aatttttctttcagagatacttctctgaagc----ttctgaactatgtttctcccaaccttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT
||| || | || | |||| || | | | || || | | || | || | || ||| ||||||| || | | ||||||||| |||||||| ||||| ||| | ||||| ||||||||||| |||||||| ||||| ||||| ||||| |||||| ||||| | || || ||| | ||||
-----gtctaacttgtcttcttttctggggaggagacaccaaattcttcctaggaattttttttttgtagcaaaacactgaactgaatta-tgaatcctttttcagGTAAATGTTACAGCTGATCACCGAATTATCTATGGTGCTGACTTGGCAGCCTTCCTTCAGACCTTTGCAAAGATCGTTGAGAACCCAGAAAGCTTGACAT
















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|89175625|gb|CI042646.1|CI042646
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|88243658|gb|CI244055.1|CI244055
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|88519780|gb|CI447434.1|CI447434
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTNCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|86502075|gb|CI144708.1|CI144708
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|88257729|gb|CI360315.1|CI360315
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGGCTGACCACAGGATTATATATGGTTCTGATTTGGCAGC
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACT-GCTGACCACAGGATTATATATGGTGCTGATTTGGCAGC
EST: gi|86496531|gb|CI139164.1|CI139164
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|58590474|gb|CF988782.1|CF988782
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|86504848|gb|CI147481.1|CI147481
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|29679375|gb|CB675650.1|CB675650
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|29289871|gb|CB483485.1|CB483485
EST:     CTTTGGTGACCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGATCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|29679373|gb|CB675648.1|CB675648
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|2311214|gb|C27369.1|C27369
EST:     CTTTGGTGGCCAACAAAGATGGTNTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|89168912|gb|CI020993.1|CI020993
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|86498936|gb|CI141569.1|CI141569
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|27547652|gb|CA767394.2|CA767394
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
EST: gi|88249651|gb|CI249500.1|CI249500
EST:     CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTG                         GTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA
genomic: CTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCA

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: 57 (upstream exon), 67 (downstream exon)
Score: 16

GGGGCTATTATGGCTGTTGGAGGATCGAGACCTACTTTGGTGGCCAACAAAGATGGTTTCTTTAGCATCAAGAACGAAATGCTGgttagtttgt ... accttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcagagatacttctctgaagcttctgaactatgtttctcccaaccttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT
                                    tttctcccaacctttt  CT-rich tract
 tatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcacatcttacctttcaacatttcactggttgcaataaatttttctttcagagatacttctctgaagcttctgaactatgtttctcccaaccttttcagGTCAATGTTACTGCTGACCACAGGATTATATATGGTGCTGATTTGGCAGCATTCCTGCAGACATTTGCGAAGATCATTGAGGATCCTGAGAGCCTAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
-gcacatc
- - - - - - - - - - - - - -tggttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct