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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttcttgttccatttctatttctctgcatatactgaaaaatggtagtgaaattatgattccatctcgcataaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGTGGACAGTCCTGCTCAGATCTTATTTATCACCGATGTCTTCCAAGAAGCT

Basic information

species Oryza sativa
transcript LOC_Os11g29370.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29370.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G574782_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------------------------------------------gtatgatttcttgttccatttctatttctctgcatatactgaaaaatggtagtgaaattatgattccatctcgcataaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGTGGACAGTCCTGCTCAGATCTTATTTATCACCGATGTCTTCCAAGAAGCT
                                                                                    |  |   ||      || | | ||   | |   || |||  ||    |    || ||  ||   |||||   ||      ||| |||||||||||||||||||| || |||||||| || || ||||| || |||||||||||  |||| |||||||| ||||||||||||||||||||||| 
gtaagctcttgatttcttgttgcagcagcctgtacttctataaaagattcaacacaagaaaaaagattttgttctctcaaatacacaaaaactaaagatatatttcttgtcccgttcat-ctgccaatctattaaaaagttgaga---catcttttat---ttacagAAACAAAAGAGAAACAAGGAGTTATTTTGAGATCTCTCAGTCACTGGGCGTGGACAGTCCATCTCAAATCTTATTCATCACCGATGTCTTCCAAGAAGCC
















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|86877415|gb|CI312773.1|CI312773
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|86522174|gb|CI162380.1|CI162380
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|89183965|gb|CI046530.1|CI046530
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACCAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|86882162|gb|CI325681.1|CI325681
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|88247082|gb|CI246931.1|CI246931
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTGGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|33683943|gb|CF312182.1|CF312182
EST:     ATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACCAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGG
genomic: ATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCA-CAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGG
EST: gi|8528131|gb|AU092946.1|AU092946
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACANNAGAGAACCAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|88835286|gb|CI370589.1|CI370589
EST:     TTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|25806482|gb|CA762443.1|CA762443
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTCGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|86483350|gb|CI125983.1|CI125983
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAGCCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|29686093|gb|CB682368.1|CB682368
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|89163810|gb|CI100700.1|CI100700
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|88968824|gb|CI098931.1|CI098931
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|88967144|gb|CI392106.1|CI392106
EST:     CTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: CTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|4716001|gb|AU057117.1|AU057117
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGGAGATTTCGCAATCACTTGGGG
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTG-AGATTTCGCAATCACTTGGGG
EST: gi|9884555|gb|BE607388.1|BE607388
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|86522877|gb|CI163083.1|CI163083
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTGGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|29671700|gb|CB667975.1|CB667975
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|11173109|gb|AU164617.1|AU164617
EST:     ATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGG
genomic: ATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACC-GGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGG
EST: gi|29615092|gb|CB620105.1|CB620105
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|87034440|gb|CI189064.1|CI189064
EST:     CACCACAACCGG                         TAACCAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: CACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|88962224|gb|CI097377.1|CI097377
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|88962181|gb|CI097334.1|CI097334
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACTAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|89163403|gb|CI100293.1|CI100293
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTCCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|427846|gb|D23987.1|D23987
EST:     ATGGTGATCTGCGCCAATACCTCTGTGGTTTCTTTGACAACCACAACCGG                         TAACCAAAAAGGAGAAACAAGGGGCTACTTT
genomic: ATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACA-CCACAACCGGgtatgatttc ... taaaccgcagTAAC-AAAA-G-AGAAACAAGGAGCTACTTT
EST: gi|86432663|gb|CI086274.1|CI086274
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|86483980|gb|CI126613.1|CI126613
EST:     TCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|3767686|gb|AU031713.1|AU031713
EST:     TATGGTGATCTGCGACAATNCCTCTGTGGTNTCTTTGACACCACAACCGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGT
EST: gi|58590134|gb|CF988442.1|CF988442
EST:     TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAAACGG                         TAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAAT
genomic: TATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAAT

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), 70 (downstream exon)
Score: 47

ACTCAAGTGGCAGCCGGGAGGCGCAAAGGCTATTATTTGGCAATACGGCCTATGGTGATCTGCGACAATACCTCTGTGGTTTCTTTGACACCACAACCGGgtatgatttc ... taaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGTGGACAGTCCTGCTCAGATCTTATTTATCACCGATGTCTTCCAAGAAGCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatatactgaaaaatggtagtgaaattatgattccatctcgcataaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGTGGACAGTCCTGCTCAGATCTTATTTATCACCGATGTCTTCCAAGAAGCT
                        aaattatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatttcttgttccatttctatttctctgcatatactgaaaaatggtagtgaaattatgattccatctcgcataaaccgcagTAACAAAAGAGAAACAAGGAGCTACTTTGAGATTTCGCAATCACTTGGGGTGGACAGTCCTGCTCAGATCTTATTTATCACCGATGTCTTCCAAGAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC