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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttgcaatttgtcttgtctttgatcatgatcaaacaagggatcatgtaagagccacttcattgtgtgttcactattttcag

Basic information

species Oryza sativa
transcript LOC_Os02g09460.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G092988_T01 (Zea mays), 5'ss of exon 2
TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttgcaatttgtcttgtctttgatcatgatcaaacaagggatcatgtaagagccacttcattgtgtgttcactattttcag
     ||||||||||| || || |||||||| |||||||||||||| ||||| || |||||||| || ||||| |||||| ||||||| ||||||||||||||    ||||| |||  ||| |        | |||   |  |  ||  ||  ||  |||| || |||   ||   |||||||
-----CACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAGgtcagtggcctaaatttttctcttctctt-------ttaaat--gctacaattaaaatgctgcttcgttatgt---catcgttttcag

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G092988_T04 (Zea mays), 5'ss of exon 2
TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttgcaatttgtcttgtctttgatcatgatcaaacaagggatcatgtaagagccacttcattgtgtgttcactattttcag
| |||||||||||||| || || |||||||| |||||||||||||| ||||| || |||||||| || ||||| |||||| ||||||| ||||||||||||||    ||||| |||  ||| |        | |||   |  |  ||  ||  ||  |||| || |||   ||   |||||||
TTCAGCACACAAGCGCATCGCTGACCATCAACGAGAACTATGACTCTGATGTGCAGGCTGACACTGAGACTTTTCTTAACAGAATTGTTCCAGAGgtcagtggcctaaatttttctcttctctt-------ttaaat--gctacaattaaaatgctgcttcgttatgt---catcgttttcag

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G17340.1 (Glycine max), 5'ss of exon 3
TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttgcaatttgtcttgtctttgatcatgatcaaacaagg-gatcatgtaagagccact--tcattgtgtgttcactattttcag---------
|||| |||||||| ||||| || |||||||||||||| |||||||  ||||| |  | ||| || ||||| ||||| ||  | || || |||||||| | |  ||  | || ||  |  | || ||  | ||  ||       |  || | |  |  |||  | | |   ||    ||||| |            
TGCATCACACAAGTGCTTCTCTTACCATCAATGAGAATTATGACTATGATGTTCGGGATGATACAGAAACCTTCCTCAATGGGATAGTTCCAGAGgttaatttttttatttagttcttacattaatatttatggaaaggtttaaatattttaaggttactgataaattattgaattctattctggatctctaata

upper sequence: LOC_Os02g09460.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA07G34680.2 (Glycine max), 5'ss of exon 3
TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttg--------caatttgtcttgtctttgatcatgat---caaacaagggatcatgtaa--gagccacttcattgtgtgttcactattttcag---
|||||||||| || ||||| || |||||||||||||| |||||||| ||||| |  |  || |||||||| ||||| || || || || || |||||   |   |         |||||||   | |   | || |   |   |         | |||||        ||  |  | ||||||| | | | |   |   
TGCAGCACACCAGTGCTTCTCTTACCATCAATGAGAATTATGACTCAGATGTTCGCGAGGATACCGAAACCTTCCTCAATCGGATAGTTCCCGAGgtttctttctttctatcaccaatttgatgtattcattattactgttctctggtgtcacaacatgtccttatatcaagttttcgtgtgtt-aatgtctcgggcag

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|88211486|gb|CI211126.1|CI211126
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|86528104|gb|CI168310.1|CI168310
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAGTTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88293128|gb|CI512893.1|CI512893
EST:     TTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: TTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|9866191|gb|AU101941.1|AU101941
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|86595369|gb|CI262607.1|CI262607
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|40493973|gb|BX901795.1|BX901795
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|86414523|gb|CI068926.1|CI068926
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GACCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88259596|gb|CI363889.1|CI363889
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88216643|gb|CI214743.1|CI214743
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAGTTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88244910|gb|CI242761.1|CI242761
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88979867|gb|CI026167.1|CI026167
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88239487|gb|CI239964.1|CI239964
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88214348|gb|CI214197.1|CI214197
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAGTTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|86495983|gb|CI138616.1|CI138616
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88243875|gb|CI242997.1|CI242997
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88543260|gb|CI473251.1|CI473251
EST:     CCGAAGCTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGGAGCACACTGTAGAAG
genomic: CCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|86483406|gb|CI126039.1|CI126039
EST:     CGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|86835521|gb|CI347978.1|CI347978
EST:     CCGATGTACAAGCTGACACCGAAACTTGCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAACACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|88213410|gb|CI213259.1|CI213259
EST:     CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: CCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
EST: gi|55411794|gb|CV724170.1|CV724170
EST:     GACACCGAAACTTTCCTTAACCGAATTGTACCAGAG                         GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG
genomic: GACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG

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: 55 (upstream exon), 34 (downstream exon)
Score: 90

TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggtt ... ctattttcagGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGCACACAAGCGCTTCCCTAACCATCAATGAGAACTATGACTCCGATGTACAAGCTGACACCGAAACTTTCCTTAACCGAATTGTACCAGAGgtcagtggttgcaatttgtcttgtctttgatcatgatcaaacaagggatcatgtaagagccacttcattgtgtgttcactattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA