Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggaacttcatcttttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG

Basic information

species Oryza sativa
transcript LOC_Os01g73310.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
gtcaggaactt-catcttttaaaccatctat---catctccaagactccaactgcatttttac-caatttgaattccttaaaattt---tgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG-
|| || |  || ||  || |      | ||    |||||             | |||| || | ||||||   |   | |  || |   | ||||| || |||||||  || ||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||||| || ||||||| 
gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 2
------------------------------------------gtcaggaacttcatcttttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
                                           | | |||     |    |      |   | |      |   |  ||    || || |   || |   || ||  |  ||| ||||||||| ||||| || |||||||| || ||||| || || || |||||| ||||  | || ||||| |||||||| ||||| |||||||| ||||||||||
gttagaagatgttttgccaattgatgagtgtttcttgtgccattgaagaagactgttcactctgtgcttgcttagtattcattgttaaatatgatattgatatatatatttttctcgatgttt-gcagGCTGGTTTTGCAGGTGATGATGCTCCTAGGGCCGTGTTCCCCAGCATTATTGGGAGACCACGCCATACTGGTGTAATGGTTGGGATGGGTCAGAAGGATG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 1
-------gtcaggaacttcatcttttaaaccatctat-----catctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
        | ||   |||  | ||||    ||| |       ||||| | || ||  |  | |||   |     ||||| |   |||| ||    |||||||| |||||||| |||||||| || |||||||| ||||| || |||||||| || ||||| ||||||||||| ||||| |||||||| || |||||||
gttagtacttagcggctttgttttttgtttcatgtgcttgtgcatctgctagccttgagtt-cataactgaatctttgatt---ttaatatggaacagGCTGGATTTGCTGGTGATGATGCTCCCAGGGCTGTCTTTCCCAGTATTGTTGGCCGACCTCGACACACTGGTGTTATGGTTGGGATGGGTCAAAAGGATG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
----gtcaggaacttcatct-----tttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
    || ||    || || |      |  |    |||| | |         | ||  || |    |||  ||    |||  |  | |||   |||||||| |||||||| |||||||| || || || || || || || ||||||||||||||| | ||||||||||||||||| || ||||| ||||| ||||
gtgagttagactgtttatttagatactgtatggttctaaccttctttgttgtacatgtgtaagactactgatcatgatttttgtatatta-acagGCTGGTTTTGCTGGTGATGATGCCCCGAGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGATG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtcaggaacttcatcttttaaaccatc-tatcatctccaagactccaactgc--atttttaccaatttgaattccttaaaattt---tgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
            |      ||| || |    |    |  | |  | | |    |  ||| |||  | ||| |  ||  |       |||   |||   |||||||||| ||||| || |||||||| || ||||| || |||||||| ||||| ||||| ||  | ||||||||||||||||| |||||||| || || ||||
gtctgttgtttctttcttgcttgatatgcagatttgttgtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcagGCTGGATTTGCGGGTGATGATGCTCCCAGGGCAGTGTTTCCTAGTATTGTGGGTCGGCCAAGGCACACTGGTGTCATGGTTGGGATGGGTCAAAAAGATG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 1
---------------------gtcaggaacttcatcttttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
                     ||   ||  |  ||  ||  |  ||   || ||||          |  |   |||| ||  |||     | || |||| | |||||||||| |||||||| |||||||| || |||||||| || || || |||||||| || ||||| ||||| ||||||||||| |||||||| || |||||||
attaaactgattctgtttgctgtggcgaggtgaat--ttgcattcagtgattatctttg-----ttagttttgttttcacacattaacgctgctcaaaaatgtgcagGCTGGATTTGCTGGTGATGATGCTCCGAGGGCTGTGTTCCCCAGTATTGTTGGCCGACCTCGACACACAGGTGTCATGGTTGGGATGGGCCAAAAGGATG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S337_21V6.2 (Physcomitrella patens), 3'ss of exon 3
---gtcaggaacttcatctttta-----aaccatctatcatctccaagactccaactgcattttt----accaatttgaattccttaaaattt--tgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
    |  | | ||| || | | |     |  |||      |   | |   |   |       | |    ||    || ||||      ||||    ||||||||| || |||||||| ||||| ||  | |||||||| || ||||||||||| || ||  | |||||||| || ||||| || ||||| |||||||| |
ctcttttgcatctttatttataatgggcagacattggatgtagactaatttatgatcaatcctctcgaaactgtgtttaattttggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------gtcaggaacttcatcttttaaaccatcta--tcatctccaagactccaactgcatttttaccaatttgaattccttaaaattt--tgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
            | | |   |||||  |  | || ||  |  | |  ||       |   |   |     |||   || ||||      ||||    ||||||||| || |||||||| ||||| ||  | |||||||| || ||||||||||| || ||  | |||||||| || ||||| || ||||| |||||||| |
caattcatgctataatggcgttcatgata-atactattcaagtgacttcagttgtgctgtccagaacgaaaccgtgtttaattgtggtgaattgaacgcagGCTGGTTTCGCTGGAGACGATGCTCCCCGCGCTGTTTTCCCCAGCATTGTTGGGCGCCCCAGGCACACTGGAGTGATGGTCGGTATGGGACAGAAGGACG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
gtcaggaacttcatcttttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
                         |          |  |  | |   || ||||| | |     |       |    | ||||||||||| ||||| ||||| ||||| || ||||| || ||||| |||||||| || || ||    ||||| || |||||||| || ||||||||||||||||
------------------------gtgcgctcctggcgcggtttcttgtggattttgatccgggggg------tgtgttcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

upper sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
gtcaggaacttcatcttttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
                         |          |  || | |   || ||||| | |     |       |    ||||||||||||| ||||| ||||| ||||| || ||||| || ||||| |||||||| || || ||    ||||| || |||||||| || ||||||||||||||||
------------------------gtgcgctcctggcgcgatttcttgtggattttgatccgggggg------tgtgtttttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG

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|88827510|gb|CI778075.1|CI778075
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|86902599|gb|CI306402.1|CI306402
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88574143|gb|CI665912.1|CI665912
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTCTTTCCTACCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88765086|gb|CI774204.1|CI774204
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88739690|gb|CI763198.1|CI763198
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88388305|gb|CI627844.1|CI627844
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTACCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|428863|gb|D25019.1|D25019
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88742905|gb|CI766413.1|CI766413
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88332048|gb|CI642273.1|CI642273
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTCTTCCCTACCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
EST: gi|88310970|gb|CI657883.1|CI657883
EST:     GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAG                         GCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT
genomic: GTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTT

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: 74 (upstream exon), 71 (downstream exon)
Score: 25

AGTAAATCTATAGGAAATGGCTGACGGTGAGGATATCCAGCCTCTTGTCTGTGACAATGGCACTGGAATGGTCAAGgtcaggaact ... aattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG
                             aatttgaattccttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaggaacttcatcttttaaaccatctatcatctccaagactccaactgcatttttaccaatttgaattccttaaaattttgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG

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