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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatattgcgatttttgcatcttatgtttatttacaagatatgtcaatactatctttttttttaaaaaaaaatcaccaatttcccttctacttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA

Basic information

species Oryza sativa
transcript LOC_Os09g34100.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G120300_T01 (Zea mays), 3'ss of exon 4
----------ttatattgcgatttttgcatcttatgtttatttacaagat--atgtcaatactatctttttttttaaaaaaaaatcaccaatttcccttctacttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
            | ||| |   |    |||||||| ||  ||       |  | || ||  |   |  |     | ||      ||   || ||  | | || || |||||||||||||||||||  | ||| |||| |||||||| ||||||||||| ||||| ||||| | | | ||||| |||||||||||||||||||||||||| ||
gtgtttgatggaaaatttcttatgactcatcttatattcgttcttgccttcaaagttaactcctgcactgcacatgaaggcttttcgttaacttttcatgtatttttattagGTCATGTGTGCTATTATTTCGCTGGTTCTGGAGCTATATTTACAGGTGACACCTTGTTCAATCTATCATGCGGAAAGCTTTTTGAAGGGACTCCACAGCA

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
-ttatatt---gcgatttttgcatc-----ttatgtttatttacaagatatgtcaatactatctttttttttaaaaaaaaatca-----ccaatttcccttctacttatatt------agGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
 | | |||   ||  | |||||||      || |  ||| |      |  ||| || |  |||| |||| |          |||     | | | | |  | || ||||| |      ||| ||| |  ||| | | || ||||||||||| ||||| ||||| || ||||| |||||||| || |||||||| ||||| |||||||| || ||||| ||
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G03320.1 (Glycine max), 3'ss of exon 4
-------ttatattgcgatt---tttgcatcttatgtttat-ttacaagatatgtcaatactatctttttttttaaaaaa---aaatcaccaatttcccttctacttatatt------agGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
       | ||  |    ||   || | |  |  | || || ||  ||  |||   || | | |  ||| |||||        |  |  | | | | |  | || ||||| |      ||| ||| |  ||| | | || ||||||||||| ||||| ||||| || ||||| ||||| || || |||||||| ||||| |||||||| || ||||| ||
gtcacattcatgctctatttgcattagtaattcttcttaatattgtaaagtattaaaaaaatctggtttcttttatgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTCAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA

upper sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 6
ttatattgcgatttttgcatcttatgtttatttacaagatatgtcaatactatctttttttttaaaaaaaaatcaccaatttcccttctacttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
|||||||  | || | |  ||  ||  ||            | ||  || ||    |||     ||   || |       ||   ||  | |   |  ||| ||  |  ||| | |||| || ||||| || ||||| |||||||||||||| ||||| ||| | |||||||| || ||||| ||||| |||||  ||||
ttatatttggcttctagattcacatagttccccctttttcttttctttattaataatttaacctaatttaattttgtgtattgattttaattgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACA

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|29686784|gb|CB683059.1|CB683059
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29646196|gb|CB651203.1|CB651203
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29640048|gb|CB645057.1|CB645057
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|396941317|gb|HO188526.1|HO188526
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|33682471|gb|CF310710.1|CF310710
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29669024|gb|CB665299.1|CB665299
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29645268|gb|CB650275.1|CB650275
EST:     TCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: TCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29645568|gb|CB650575.1|CB650575
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29645986|gb|CB650993.1|CB650993
EST:     TAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: TAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29656927|gb|CB653202.1|CB653202
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|33680534|gb|CF308773.1|CF308773
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29645569|gb|CB650576.1|CB650576
EST:     -TTGCTGGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: TTTGCT-GGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29663513|gb|CB659788.1|CB659788
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
EST: gi|29663511|gb|CB659786.1|CB659786
EST:     GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAG                         GTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA
genomic: GTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACA

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: 75 (upstream exon), 74 (downstream exon)
Score: 61

GATAGAATTCCAGGCATTGACATAACTCTTAGTGAGGGTGACACATGGATGTTTGCTGGTCATCAAGTTCTTGTAATGGAAACTCCTGGTCATACATCAGgtgcgtgctt ... cttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatactatctttttttttaaaaaaaaatcaccaatttcccttctacttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
                                  tttcccttctacttat  CT-rich tract
     tatctttttttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatattgcgatttttgcatcttatgtttatttacaagatatgtcaatactatctttttttttaaaaaaaaatcaccaatttcccttctacttatattagGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - ttttgca
- - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa