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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_Os11g43620.2
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|87018205|gb|CI297418.1|CI297418
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|86418484|gb|CI032693.1|CI032693
EST:     CGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|117223750|gb|CT842091.1|CT842091
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|86537089|gb|CI177295.1|CI177295
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|55442446|gb|CV734541.1|CV734541
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|55439258|gb|CV732932.1|CV732932
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|55439260|gb|CV732933.1|CV732933
EST:     AGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: AGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|8528391|gb|AU093206.1|AU093206
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc
EST: gi|15846851|gb|BI795127.1|BI795127
EST:     C-GCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATG                         ACTGTTCCAGTTAACCC-AAACCTTTCTTGAACAACCTGACAGGGAAGCCT
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGgcggtaatac ... cttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCT
EST: gi|163921024|gb|EG710124.1|EG710124
EST:     CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAATGGCG                       
genomic: CGGCGGCGGAGCGGAGGAGCACGGCGAGCTAGCTGCTCTACCTTGGAAT---Ggcggtaatac ... cttaatgc


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttatacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG
                                            tcttaat  putative branch site (score: 3)
                                       ttgtttctt  CT-rich tract
                                          tttcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatgtacacattgaatttgcttgtaacagatggaatttcgttctttttatacatctttcctgttctgctcttaatggatggattgtttcttaatgcagACTGTTCCAGTTAACCCAAAACCTTTCTTGAACAACCTGACAGGGAAGCCTGTCATTGTCAAACTTAAGTGGGGTATGGAATACAAAG

- - tgtacac
- - - - - - - - - ttgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggatg