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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcttaaggaaatctgattcctttttctttacatatatgacaagccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG

Basic information

species Oryza sativa
transcript LOC_Os01g51920.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G425249_T01 (Zea mays), 3'ss of exon 3
gtttcttaaggaa-----atctgattcctttttctttacatatatgacaagccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG
||||   |    |     || |||     | | || |   |  ||   |||       |   |     |  || |   |  | | ||||  |  | |    |||||||||||| ||||| |||||||| |||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||||   ||||| |||| |||||
gttttggagactactactatgtgaagatatatgctctctgttcata--aagtttttgcttcgtaccaacctttcgtaacagtgtcttctctttttgt---cacagGATTATGAGTATGCAAGCTTCAACCCAGTTGCATATGACATTGCTAACCATTTCTGTGAGATGGCAGCAGACTATCATTCATCAAAGCCTCATATACTGG

upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv13s0084g00150.t01 (Vitis vinifera), 3'ss of exon 4
-----gtttcttaaggaaatctgattcctttttctttacatatatgacaagccccaa--ttaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG
      |  ||| |    |        ||| |        ||    | |       |  |||| |    |  |||       ||||| |||  | |        ||||||||||| ||||| || | |||||| ||  | |||||||| || ||||| ||||| |||||||| || ||||||||| |||| | ||| || |   |||
tgactatcacttgatatgaatcaggcacttgtctgccttttagtcaatatttttggagcttaactagctgttattcatctaattctgctctctttac-------cagGATTATGAGTATGCAAGTTACAATCCTGTCACTTATGACATAGCAAATCACTTCTGTGAGATGGCTGCTGACTATCATACAGAAACGCCTCACATTTTGG

upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ23622 (Selaginella moellendorffii), 3'ss of exon 3
----gtttcttaaggaaatctgattcctttttctttacatatatgacaagccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG
    |||||||       ||     | |||| |||     || |       |    ||| || ||  |||| | ||      || |  |           |||||| || || || ||||||| |||||| || |||| |||||| || ||||| |||||||||||||| || || |||||  | ||    || ||  | ||||
gtgcgtttctt-------tcaaggcctttttgcttggtggatcttctttctcttctttagtt-ttctcaatctaattaacgttggtgctta---------acagGACTACGAGTACGCCAGCTACAATCCCGTGGCGTTTGACATTGCGAATCACTTCTGCGAGATGGCTGCCGATTATCACACGGAATCTCCCCACCGGCTGG

upper sequence: LOC_Os01g51920.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ05852 (Selaginella moellendorffii), 3'ss of exon 3
----gtttcttaaggaaatctgattcctttttctttacatatatgacaagccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG
    |||||||       ||     | |||| |||     || |       |    ||| || ||  |||| | ||      || |  |           |||||| || || || ||||||| |||||| || |||| |||||| || ||||| |||||||||||||| || || |||||  | ||    || ||  | ||||
gtgcgtttctt-------tcaaggcctttttgcttggtggatcttctttctcttccttagtt-ttctcaatctaattaacgttggtgctta---------acagGACTACGAGTACGCCAGCTACAATCCCGTGGCGTTTGACATTGCGAATCACTTCTGCGAGATGGCTGCCGATTATCACACGGAATCTCCCCACCGCCTGG

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|86497719|gb|CI140352.1|CI140352
EST:     GGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: GGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|33684238|gb|CF312477.1|CF312477
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|325494505|gb|JG459029.1|JG459029
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGAATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|58672419|gb|CK061105.1|CK061105
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|33381326|gb|CF196669.1|CF196669
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GTGAGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAA
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagG--A--TTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAA
EST: gi|33675298|gb|CF303537.1|CF303537
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|58588260|gb|CF986568.1|CF986568
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|33676500|gb|CF304739.1|CF304739
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|33679472|gb|CF307711.1|CF307711
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|40488156|gb|BX898760.1|BX898760
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTA-TCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|2311781|gb|C27936.1|C27936
EST:     AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATC                         GATTATNAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: AGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
EST: gi|33676093|gb|CF304332.1|CF304332
EST:     GTTGACTATCATC                         GATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT
genomic: GTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCAT

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), 63 (downstream exon)
Score: 51

AGAATTTTCAGGGGATTACCACGGGATTGGTTTTTGCCACAACGATCTTCAGTATGGCAACATCATGATTGATGAAGACACCAACATGTTGACTATCATCgtgagtaata ... atatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG
                          tcctttctgttcttct  CT-rich tract
                                      ttctcatatatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcttaaggaaatctgattcctttttctttacatatatgacaagccccaattaattgttggcaatttgatcctttctgttcttctcatatatatacagGATTATGAATATGCCAGCTTCAATCCAGTTGCGTATGACATCGCTAATCATTTCTGCGAGATGGCAGCAGACTATCATTCAGAGAAGCCACATAGACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - taaggaaa
- - - - - - - -ctgattc
- - - - - - - - - - - - - - - - - - - - - caagccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggc