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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatattgtacttatttctaagttaatcacaacatatttacctttctagcgtcatgacattttgacaagcacatctatcactgatatatggctactgtaattgttactgattgcttgttccaactatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATGGACAGTTGATGTGCCAAATGTTCTCGCATTCGTGAAGGAACTCCTCATG

Basic information

species Oryza sativa
transcript LOC_Os08g44370.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G085960_T02 (Zea mays), 3'ss of exon 8
gtatgatattgtacttatttctaagttaatcacaacatatttacctttctagcgtcatgacattttgacaagcacatctatcactgatatatggctactgtaattgttactgattgcttgttccaactatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATGGACAGTTGATGTGCCAAATGTTCTCGCATTCGTGAAGGAACTCCTCATG
                                      | | | |   | |  |  |          ||| |   || | |||   | || |   |     ||||||| |    |||||||||| ||||||  ||||||||||||||||||| || ||||| || || || || || |||||||||||||| |||||||||||||| ||| | |  || || ||| | || ||||||
--------------------------------tcttggagtaagcaaaccaaggcaaaagttaccccacaggactatgtttcaacaa-atttctatttcacaattgtttc----tgcttgttcctactatggtgcagGTGGAATTCAGAGAACCCTTGGTCAGGGTATAAACCGATTTCAGTTGCATGGACGGTTGATGTGCCAAAGGTTATTGGCTTTGTAAAGAAGCTGCTCATG

upper sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G015344_T01 (Zea mays), 3'ss of exon 8
gtatgatattgtacttatttctaagttaatcacaacatatttacctttctagcgtcatgacattttgacaagcacatctatcactgatatatg-gctactgtaattgttac-----tgattgcttgttccaactatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATGGACAGTTGATGTGCCAAATGTTCTCGCATTCGTGAAGGAACTCCTCATG
                                          | |||| | | || |  | |    | |||      |      |||| |||  | | | | |  | | ||     |   | ||||||||  |||||  ||||||||||||||||||| |||||||| || || || || || |||||||||||||| |||||||||||||| ||  ||   ||  | ||| | || ||||||
------------------------------------------aacttt-tggagtaagcaaaccaaggcaaaagttaccccacatgatctatatgtttcagcagatttcacacttgtttcttcttgttcctcctatgctgcagGTGGAATTCAGAGAACCCATGGTCAGGGTATAAACCGATTTCAGTTGCATGGACGGTTGATGTGCCAAAGGTCATCAGCTTTATAAAGAAGCTGCTCATG
















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|27920535|gb|CB096343.1|CB096343
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|89175000|gb|CI041078.1|CI041078
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|38471404|gb|CF955535.1|CF955535
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29658032|gb|CB654307.1|CB654307
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|58604658|gb|CK015186.1|CK015186
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29670960|gb|CB667235.1|CB667235
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614111|gb|CB619124.1|CB619124
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614071|gb|CB619084.1|CB619084
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614027|gb|CB619040.1|CB619040
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29623183|gb|CB628194.1|CB628194
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614082|gb|CB619095.1|CB619095
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614023|gb|CB619036.1|CB619036
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|38481551|gb|CF965640.1|CF965640
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|163920050|gb|EG712004.1|EG712004
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|4716626|gb|AU057742.1|AU057742
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614069|gb|CB619082.1|CB619082
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614109|gb|CB619122.1|CB619122
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|4716625|gb|AU057741.1|AU057741
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|86872650|gb|CI323053.1|CI323053
EST:     GCACTGGTCACAC-GTAATGGACCAAGGATT-AGAAA                         GTGG-ATTCAGAG-ATCCAT-GTCTGGCTACAAGCCAATCTCAGGTGCATG
genomic: GCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|29614025|gb|CB619038.1|CB619038
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|11564758|gb|AU165394.1|AU165394
EST:     NCCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|89183746|gb|CI046311.1|CI046311
EST:     ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: ACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
EST: gi|27554072|gb|CA997972.1|CA997972
EST:     GGTCACACTTTAATGGACCAAGGATTGAAAAA                         GTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG
genomic: GGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATG

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), 73 (downstream exon)
Score: 49

TAGTTCACCCTGAGTACTTCACGTTCAAGAAGGGTGTTGTGAGAGTAGAAACCCAGGGCATTTGCACTGGTCACACTTTAATGGACCAAGGATTGAAAAAgtatgatatt ... tatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATGGACAGTTGATGTGCCAAATGTTCTCGCATTCGTGAAGGAACTCCTCATG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgatatatggctactgtaattgttactgattgcttgttccaactatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATGGACAGTTGATGTGCCAAATGTTCTCGCATTCGTGAAGGAACTCCTCATG
                         tactgat  putative branch site (score: 49)
                  taattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatattgtacttatttctaagttaatcacaacatatttacctttctagcgtcatgacattttgacaagcacatctatcactgatatatggctactgtaattgttactgattgcttgttccaactatgacgcagGTGGAATTCAGAGAATCCATGGTCTGGCTACAAGCCAATCTCAGTTGCATGGACAGTTGATGTGCCAAATGTTCTCGCATTCGTGAAGGAACTCCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC