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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatgtacacattgaatttgcttgtaacagatggaatttcgttctttttatacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG

Basic information

species Oryza sativa
transcript LOC_Os11g43620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G058252_T01 (Zea mays), 3'ss of exon 1
acaatgtacacattgaatttgcttgtaacagatggaatttcgttcttt--ttatacatc-tttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
   ||  | | | |||| |   |  |   |  |    || |  ||  |  | |   ||  | |   | | |   || | |  ||    | |   ||  ||||||| |||||||||||||||||||||||  |||||||||||||||| |||||||| ||||||||||| |||||||||||||| ||||| |
--gatccaaagaatgaaatgagtcttgttatgtatgtttgcaatccataataaagtatggtcttacggtatatactcactt-atcagctctcgttttgtgcagACCGTTCCAGTTAACCCAAAACCTTTTCTGAACAACCTGACAGGAAAGCCTGTTATTGTCAAACTCAAGTGGGGTATGGAGTACAAGG

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G168252_T01 (Zea mays), 3'ss of exon 1
acaatgtacacattgaatttgcttgtaacagatggaatttcgttctttttat--acatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
|  |  |     ||| | |  ||||| |   |||     | | | |  | |   | |   ||    | |   |  | |  ||   | | |   ||   ||||||||| ||||||||||||||||||||| ||||||||||||| ||||||||||| ||||||||||| |||||||||||||| |||||||
atgaaatgagtcttgcact--cttgttatttatgtttgctagctataataaaggaaaatcttatgatacacgtgctcaccgagcaactctcgttttgagcagACTGTGCCAGTTAACCCAAAACCTTTCCTGAACAACCTGACGGGGAAGCCTGTAATTGTCAAACTCAAGTGGGGTATGGAGTACAAAG

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G07060.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------------acaatgtacacattgaatttgcttgtaacagatggaatttcgttcttttta--tacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
                                                                                    || |  |   |    | ||||  |     | |||  ||   |  | |   ||  | |  | | || |    || ||    |   |  |  ||  |||||||| | |||||||| || || ||||||||||||||  |||| ||||||||||| ||||| ||||| |||||||| ||||| ||||| |
gtgagtaccttcttcttgcactccctttacttaatcatcttccatttatttcattcacttaacctgcatcttcataactgagtgatttcaatgcttg-ctcgctttgagtgtgtagaaggtcacacgatgtgattaattgtgccttattttctaatttattttcgtcctcgtgttttttgcagACTATACCAGTTAATCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCTGTAATTGTGAAACTGAAGTGGGGAATGGAGTACAAGG

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G21250.1 (Glycine max), 3'ss of exon 1
acaatgtacacattgaatttgcttgtaacagatggaatttcgttcttttta--tacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
    ||  |   || |||   |   |      | |||  ||   |  | |   ||  | |  | | || |    || ||   |||  |   | ||  |||||||| ||||||||||||| || ||||||||||||||  |||| |||||||| || ||||| ||||| |||||||| ||||| ||||| |
-agctgagcgatttcaatgctcacattgagtgtagaaggtcacacaatgtgattaattgtgccttattttttaatttattc-tggtcttcctgtttttgcagACTATTCCAGTTAACCCCAAGCCTTTCTTGAACAATTTGACTGGGAAGCCCGTAATTGTGAAACTCAAGTGGGGAATGGAGTACAAGG

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G30220.1 (Arabidopsis thaliana), 3'ss of exon 1
---acaatgtacacattgaatttgcttgtaacag--atggaatttcgttctttttatacatctttcctgttctgctctta-atggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
     ||  | |||| ||  |||   |  ||  |  |||   ||  |||| ||  ||   | |||  ||  |     ||  ||| |||   ||| | ||   ||||||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| |||||||||||||
gttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagtttgtatgtatg---tgtgtttt---gcagACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAATGGAATACAAAG

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G30220.2 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------acaatgtacacattgaatttgcttgtaacag--atggaatttcgttctttttatacatctttcctgttctgctctta-atggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
                             ||  | |||| ||  |||   |  ||  |  |||   ||  |||| ||  ||   | |||  ||  |     ||  ||| |||   ||| | ||   ||||||| |||| |||||||| ||||| |||||||||||| |||| || ||| |||| || ||||| ||||| ||||| |            
cataaaaattgcattcgagaattcgttggaaaatgcacaatgtgtttatcttcaaatgtgatgcttttgagttcattccattagtatttgatgaaccaagTTTGTATGTATG---TGTGTTTT---GCAGACTATTCCGGTTAACCCGAAACCATTCTTGAACAACTTGACCGGCAAGACTGTTATCGTCAAGCTTAAATGGGGAA------------

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0220g00030.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------------------acaatgtacaca-ttgaatttgcttgtaacagatggaatttcgttctttttata-------------catctttcctgttctgctctta-atggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
                                                             | |  | |   ||   || |  || |  | |  |||  |  |||     | |              |    ||  |   || ||||| ||| |||  |||||   |  ||||||| || ||| | ||||| || || |||||||| ||| |||| ||||||||||||||||||||||| |||||||| ||||| |||||||
gtaagtagttgattttatttatttatttttaagttattattattaattttcgtggagaattatttcataaggttatgttcgtctgcaggaaagagaaaatttttcccgagaaaaaaaaaaaaaaaatagaaatctggaaatgttcttatatgaatg--ttgttatgtt-tgcagACCGTACCACTGAACCCTAAGCCCTTCTTGAATAACTTGACTGGGAAGCCTGTCATTGTCAAACTCAAGTGGGGAATGGAGTACAAAG

upper sequence: LOC_Os11g43620.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S46_244V6.1 (Physcomitrella patens), 3'ss of exon 1
--------acaatgtacacattgaatttgcttgtaacagatggaatttcgttctttttatacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
         ||   |      ||| ||   ||   |||||| ||| |  ||    ||   |  | | |  |||| |  | ||  |   ||   | ||      |||||||  | || || || || ||||| || |||||| || ||||||||||||| || || || ||||| |||||||| |||||||||||||
tgttgtttgcatactttcttatgacttgtttttcgacagattgaagtgagtgtgatt---atttttgttttgttttcgttttgttttgtgagctctt-----gtgcagACCATCCCCGTGAATCCGAAACCCTTTTTGAACGACTTGACAGGGAAGCCGGTGATCGTGAAACTGAAGTGGGGGATGGAATACAAAG

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|2442205|gb|C73976.1|C73976
EST:     GTCGGAG-GGATGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: GGCGGAGCGGA-GGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|86537089|gb|CI177295.1|CI177295
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|55439260|gb|CV732933.1|CV732933
EST:     AGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: AGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|15846851|gb|BI795127.1|BI795127
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---G                         ACTGTTCCAGTTAACCC-AAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|86418484|gb|CI032693.1|CI032693
EST:     CGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCCAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|55439258|gb|CV732932.1|CV732932
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|8528391|gb|AU093206.1|AU093206
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|163921024|gb|EG710124.1|EG710124
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCC
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACT-GTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCC
EST: gi|87018205|gb|CI297418.1|CI297418
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|55442446|gb|CV734541.1|CV734541
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|426828|gb|D22902.1|D22902
EST:     CGGCGGA-NGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|117223750|gb|CT842091.1|CT842091
EST:     CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                         ACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT

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: 13

ACCAACCCCTCGCTCTCCCACTCATCTCGTCGGCGGCGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCGgtaataccct ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
                                            tcttaat  putative branch site (score: 13)
                                       ttgtttctt  CT-rich tract
                                          tttcttaat  TA-rich tract