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'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g45650.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM5G813909_T01 (Zea mays), 3'ss of exon 13
tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaa-tttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG
 | | ||  |     | ||||||  |    |     || |  | |  | |  ||    | ||||||||     | | |  |   ||     ||| |||||||| |||||||| ||||| |||||||| ||||| |||||||| || || ||||||||||| ||||| || || || |||||    |||||||||||  |||
ccttcctaacaaga-ttgttgtttatcccacataccgttatatacttatatagccacaagatttgcattcagcactctaaagcatgtacaaaaaatttcagGAGGAGAACTTGTCTGCGATGAACACCGATCCTTGGTATTCGGCATATCACTACTCCCACCCACCACTCGTCGAGAGGCTGCAAGCTCTTGAAGATTCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G702159_T01 (Zea mays), 3'ss of exon 14
--tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgca--caaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG
       ||||    |   |||| |  | |   |||  ||  | | ||  || |    |||||  ||     |||  |   || |   ||     ||||||||||| |||||||| |||||||||||||| ||||| |||||||| || || ||||||||||| ||||| || || ||||||||    |||||||||||  |||
gggatccctgttcacttgtgttgctattttgtgcctccgtagcatacagccacatgagttgca--ttcattcagc--acgctgaagcatgtcaaaaaatttcagGAGGAGAACTTGTCTGCAATGAACACCGATCCTTGGTATTCGGCATATCACTACTCCCACCCACCTCTCGTCGAAAGGCTGCAAGCTCTTGAAGATTCAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT4G01320.1 (Arabidopsis thaliana), 3'ss of exon 13
tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgca-aatttgcatagcctaatt---tggaatttgctttcaaattt--cagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG
                    ||  |    |              ||||||||| |  |  ||||||  |  |  | ||   |||| |||   ||   ||||  ||||||||||||||||| ||||||||||| ||||| | ||| ||||| || |||||||| ||||| || ||||||||||||||    ||  |||| |  | ||
--------------------gtcagagaagataacaacaga--acacaaactgttacctcaatttgtgtcacacacttaaatggattttttgttgggattttgcagGAAGAGAACTTATCAGCAATGAACACTGATCCATTGTACTCAGCTTATCACTACTCACATCCTCCTCTTGTTGAAAGGCTTCGAGCCATTGATGGAGAAG

upper sequence: LOC_Os02g45650.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv15s0046g02040.t01 (Vitis vinifera), 3'ss of exon 13
tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG
 |  |   | |         | |  | |||         ||    |||   |  |||  ||    | |    || |    ||     |      || |||||||| || || || || ||||| |||||||| ||||| ||||| |||||||| || ||||| || |||||||||||  |  |||| ||||| ||  | |
acccaaaattgtcaggaagaggtttttttgagtgcaagtactcttacatgttttttgtgaaaccccgtgcattactcaacaaagatttaatgttttccagGAAGAAAATTTGTCGGCTATGAATACAGATCCATGGTACTCAGCTTACCACTATTCACATCCTCCACTTGTTGAAAGATTGGCTGCACTTGATGAACCCG

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|88215064|gb|CI214913.1|CI214913
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCATGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88489314|gb|CI426586.1|CI426586
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88831123|gb|CI080547.1|CI080547
EST:     AGAACCTGGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88536315|gb|CI466060.1|CI466060
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88526548|gb|CI454616.1|CI454616
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88994093|gb|CI116057.1|CI116057
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCCATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88248064|gb|CI246682.1|CI246682
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|15847722|gb|BI795998.1|BI795998
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTTCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|86903727|gb|CI300581.1|CI300581
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|86487701|gb|CI130334.1|CI130334
EST:     CTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTAATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: CTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|86259979|gb|CI065852.1|CI065852
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|86865883|gb|CI335514.1|CI335514
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88285767|gb|CI510027.1|CI510027
EST:     AACCTGGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|86490395|gb|CI133028.1|CI133028
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88223219|gb|CI223068.1|CI223068
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|5003204|gb|AU068353.1|AU068353
EST:     AACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88845492|gb|CI084417.1|CI084417
EST:     AGAACCTGGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|29634138|gb|CB639147.1|CB639147
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAN
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88480857|gb|CI418128.1|CI418128
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|88837192|gb|CI078552.1|CI078552
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|89177897|gb|CI391076.1|CI391076
EST:     AGAACCTTGGGTATCCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
EST: gi|89171171|gb|CI109695.1|CI109695
EST:     AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAG                         GAAGAGAACTTATGTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC
genomic: AGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCAC

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), 73 (downstream exon)
Score: 47

GCTGATGCTTTTGCCAAGAACCTTGGGTATGCTCCTCAGCTCCGTGCAGCCCTTGTTAAACTACAGgtaaccatcg ... caaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG
                        gcctaat  putative branch site (score: 47)
                                     tttgctttc  putative PPT
                                          tttcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtactgtcggttctcgttgttcgtattgcccttggtcacctgcacaaactgcttgcaaatttgcatagcctaatttggaatttgctttcaaatttcagGAAGAGAACTTATCTGCAATGAACACAGATCCGTGGTATTCAGCCTACCACTACTCCCATCCACCCCTTGTTGAAAGGCTCTCTGCTCTTGAAGACGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
-cgtactg
- - - - - - - - - - - - - - tgccctt
- - - - - - - - - - - - - - - - - - - -acctgca
- - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcata