Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgattatatgcttatcaatgaattaggtttctcttctaatacacaaactaaataactcttctgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAGGATGAAAATGTCAGGCTTTCTCCACCACGATTG

Basic information

species Oryza sativa
transcript LOC_Os01g54910.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G128688_T01 (Zea mays), 3'ss of exon 16
gtaagttgattatatgcttatcaatgaat-taggtttctcttctaatacacaaactaaataactcttctgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAGGATGAAAATGTCAGGCTTTCTCCACCACGATTG
||| | || | | || |  ||||  |  | |   ||||||||   ||||   || | |||  |||||  |     ||| | ||||||||||||||||||||||||||||| || ||||| || |||||||||||||||||| |  | |||||||| ||||||
gtatgatggtcaaatacaaatcacggcctatttctttctctttctatacttgaagttaatgtctctttgg-----cagGTGAATCCTGTGAGAACTAAAGAACTTACAAATATCCGAGCCCCTGGAAAGGATGAAAATGTCCGTTTGTCTCCACCCCGATTG
















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|58668676|gb|CK057362.1|CK057362
EST:     CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|88561572|gb|CI492289.1|CI492289
EST:     CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|87040973|gb|CI195595.1|CI195595
EST:     TGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACANACATTCGAGCTCCAGGAAAG
genomic: TGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|33681847|gb|CF310086.1|CF310086
EST:     CGTACGAAGGCATGATTGTTGGAGAGTACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCA
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCA
EST: gi|58681400|gb|CK070087.1|CK070087
EST:     CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTAACAAACATTCGAGCTCCAGGAAA
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTA-CAAACATTCGAGCTCCAGGAAA
EST: gi|25806199|gb|CA762160.1|CA762160
EST:     GAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: GAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|218480472|gb|FG958725.1|FG958725
EST:     CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAA
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAA-
EST: gi|58690249|gb|CK078936.1|CK078936
EST:     CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|88955134|gb|CI721765.1|CI721765
EST:     GTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: GTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|29629970|gb|CB634979.1|CB634979
EST:     CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: CGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
EST: gi|88904755|gb|CI712054.1|CI712054
EST:     GTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGAT                         ATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG
genomic: GTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAG

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: 51 (upstream exon), 67 (downstream exon)
Score: 27

GCGTACGAAGGCATGATTGTTGGAGAGCACTCACGTGACAGTGATCTTGATgtaagttgat ... tgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAGGATGAAAATGTCAGGCTTTCTCCACCACGATTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgaattaggtttctcttctaatacacaaactaaataactcttctgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAGGATGAAAATGTCAGGCTTTCTCCACCACGATTG
                                 aaataac  putative branch site (score: 27)
                                       ctcttctgttgttc  CT-rich tract
                            aaactaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgattatatgcttatcaatgaattaggtttctcttctaatacacaaactaaataactcttctgttgttcagATCAATCCTGTGAGAACTAAAGAACTTACAAACATTCGAGCTCCAGGAAAGGATGAAAATGTCAGGCTTTCTCCACCACGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG