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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgagccatgagacacttccaaatgagcaccaagctgtaccgacaatctggcattccctgatttcttctgcgctgactcctcccttacgatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATCGCTGGGCTTTTCGGCAAAGACATCTCACCTGTGAGTGCTGCGTAAAGTC

Basic information

species Oryza sativa
transcript LOC_Os04g39270.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g39270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G169516_T05 (Zea mays), 3'ss of exon 9
gtaag---tgagccatgagacacttccaaatgagcaccaagctgtaccgacaatctggcattccctgatttc--ttctgcgctgactcctcccttacga-tgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATCGCTGGGCTTTTCGGCAAAGACATCTCACCTGTGAGTGCTGCGTAAAGTC
|||||   |||| ||  ||| || |  |||    ||||| |||  || | | |   || ||||| |  | |   | |||   |||||||||| ||  |  || ||||||||||||| ||||| || |||||||||||||||||||| || ||||||||||||||||||||||||||||| ||||| | ||   ||||| | || || |
gtaagccatgagacac-agatacctgtaaactgacaccaggctcaactg-cgactcggtattcctttctcttcgtactgatatgactcctccgttgtgtctgttgtagGTTCTCGTCGGGGAATCCCTCATCAAGCAGGAGGATCCAGGGAAAGCAATCGCTGGGCTTTTCGGCAAAGATATCTCGCATGCTGGTGCTACCTAGAGAC
















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|88906967|gb|CI376039.1|CI376039
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|325494562|gb|JG459086.1|JG459086
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         T
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtag-
EST: gi|325494562|gb|JG459086.1|JG459086
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         T
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtag-
EST: gi|4714825|gb|AU055942.1|AU055942
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|29616384|gb|CB621396.1|CB621396
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|4714826|gb|AU055943.1|AU055943
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|88986358|gb|CI033589.1|CI033589
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCCAAGCCATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|86850836|gb|CI338812.1|CI338812
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|66930116|gb|CX116964.1|CX116964
EST:     CGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: CGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|29663297|gb|CB659572.1|CB659572
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
EST: gi|86849316|gb|CI297783.1|CI297783
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGC
EST: gi|29615583|gb|CB620595.1|CB620595
EST:     TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCT                         GTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC
genomic: TGTTCACACCAGACCATATTTCATTCGTTCAGAATGCTGGGGTTAAAGCTgtaagtgagc ... gatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatctggcattccctgatttcttctgcgctgactcctcccttacgatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATCGCTGGGCTTTTCGGCAAAGACATCTCACCTGTGAGTGCTGCGTAAAGTC
                                      cccttac  putative branch site (score: 3)
                 atttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgagccatgagacacttccaaatgagcaccaagctgtaccgacaatctggcattccctgatttcttctgcgctgactcctcccttacgatgctgtagGTTCTCGTTGGGGAGTCTCTCATCAAGCAGGAGGATCCTGGCAAAGCAATCGCTGGGCTTTTCGGCAAAGACATCTCACCTGTGAGTGCTGCGTAAAGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC