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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaatttactcgtccctcagttcttgctgcaacgacagccatcaaagtctattgctccatttctgagaacttatagcgttcagatattgcataattcacactattgcatatgtttcatgtttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTTCATCGCCTTTGTTTCTACGGAAGCAGAGGCTGACAAGCCTGAGATCGAG

Basic information

species Oryza sativa
transcript LOC_Os03g16900.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G09550.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaagcaatttactcgtccctcagttcttgctgcaacgacagccatcaaagtctattgctccatttctgagaacttatagcgttcagatattgcataattcacacta--ttgcatatgtttcatgtttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTTCATCGCCTTTGTTTCTACGGAAGCAGAGGCTGACAAGCCTGAGATCGAG
                    | || || |  | |||  |||  |||  || | ||  |   |||   ||  | || ||    |||   | |   | | || |   ||  |  | |  ||||   | ||  ||  |||||| |||||||||||||||| |||||||| || |||||||| ||||| | ||| || ||||| ||| | ||||| ||  ||||||| || ||    |||
-------------------gtaagatcatagt-caagaaca--cattcaaat-tacagaaacatgcatgt-atctgatttgtttctactttgaaacagttgaagataaatctcttgagtttttggatt--ttgtagGTACTTGTTCTGTTGCTCATACGCTCACAATGTGGCACCAAAGGGCAAATACATAGCTTTTGTCTCTGCAGAAGCTGAAACTGACAATCCAGAAGAGGAG

upper sequence: LOC_Os03g16900.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S85_191V6.1 (Physcomitrella patens), 3'ss of exon 10
gtaagcaatttactcgtccctcagttcttgctgcaacgacagccatcaaagtctattgctccatttctgagaacttatagcgttcagatattgcataattcacactattgcatatgtttcat--gtttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTTCATCGCCTTTGTTTCTACGGAAGCAGAGGCTGACAAGCCTGAGATCGAG
                                |    |   ||     |||| |  || |   |    | | | || |   || | ||  |||  |  |     | || ||  | |||| ||   |  |||  |||||| ||||||||||| ||  |  |||||||||| || || |||||||||| |||||| ||||||||  |||| |  ||| | || || ||||||   |||
--------------------------------gatgtggtggctggtgaagtgttatgtttggtc---gtgcatttctctggtacggagtttgtgtggtgtgttcgat-gctgacgtttgatcgatacggtggcagGTATGTGTTCTGTTGTTCTCACTCTCACAACGTGGCTCCGAAAGGCAAGTACATCGCGTTTGTTTCAGCGGAGGTGGAGACGGAGAACCCTGAGGCTGAG
















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|8856777|gb|AU094095.1|AU094095
EST:     CCCGTGCAGATCATCCTCCCAAAGAAACAG-TGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|33693913|gb|CF322152.1|CF322152
EST:     TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|89197962|gb|CI117440.1|CI117440
EST:     GAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: GAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|87026816|gb|CI259469.1|CI259469
EST:     TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|87026825|gb|CI259478.1|CI259478
EST:     TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|86879928|gb|CI339995.1|CI339995
EST:     CAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: CAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|3761371|gb|C98619.1|C98619
EST:     CCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: -CCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|88996545|gb|CI260049.1|CI260049
EST:     TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
EST: gi|33693914|gb|CF322153.1|CF322153
EST:     TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACAT                         GTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT
genomic: TCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTT

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: 66 (upstream exon), 75 (downstream exon)
Score: 16

GTGCAATATGCATAATGAAGCATCCGATTCCTGACACCAAGGATTCTCATTCCGTGCAGATCATCCTCCCAAAGAAACAGCTGAAGCGCAAATCAGACATgtaagcaatt ... ttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTTCATCGCCTTTGTTTCTACGGAAGCAGAGGCTGACAAGCCTGAGATCGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgttcagatattgcataattcacactattgcatatgtttcatgtttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTTCATCGCCTTTGTTTCTACGGAAGCAGAGGCTGACAAGCCTGAGATCGAG
               ataattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaatttactcgtccctcagttcttgctgcaacgacagccatcaaagtctattgctccatttctgagaacttatagcgttcagatattgcataattcacactattgcatatgtttcatgtttggtttcagGTACGTGTTCTGTTGCTCATATGCTCACAACGTTGCACCAAAAGGCAAGTTCATCGCCTTTGTTTCTACGGAAGCAGAGGCTGACAAGCCTGAGATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC