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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatgaattgttgcattttccaaaaaaataattccatctctaatgctgttgctgtgtaattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA

Basic information

species Oryza sativa
transcript LOC_Os06g13810.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G059151_T01 (Zea mays), 3'ss of exon 11
------------------------------gtatgtatgaattgttgcattttccaaaaaaataattcca--tctctaatgctgttgctgtgtaattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA
                               | | ||| |||| |||| ||| |||||    |  |||||  ||||| |||| | | || ||  |||| |||| || ||||||||||| ||||||||||||| |||||||||||||||||||||||| |||||||| ||  |||| || ||||||||| ||||||||||||||
gccagggaatgtcatctccctgtggtggttttttctattaatt-ttgcgttt-ccaaatttttctttccaactctctcatgcagcttctttgctattt-gcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGCGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G143862_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------------------gtatgta-tgaattgttgcattttccaaaaaaataattccatctctaatgctgttgc----tgtgtaattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA
                                                                                                                    |  ||| |  | | ||  | |    |   |   |||  |||||| ||  || |         | |  | |||||| || ||||||||||| ||||||||||||| |||||||||||||||||||||||| |||||||| ||| |||| || ||||||||| ||||||||||||||
gtaagcgttttttttttaattttgtgaactgagcaataacttggttggtagacttcccactgaggaggccacccctgagaattagtttcagggagttccctggccagctagggttttgggtactccacttttttaatacaaagccatgaaatgtcatctccaactctctcatgtagcttttgttattgcagGTACGAAGGAAGATGCGGCCTTCCTACTAATTTTGATTCTAACTATTGCTATGCATTAGGCTATGGTGCTGGTGCCCTTCTCCAAAGTGGGAAGACAGGA

upper sequence: LOC_Os06g13810.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------------------------------------------------------------------gtatgtatgaattgttgcattttccaaaaaaataattccatctctaa---tgctgttgctgtgtaattt------tgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA
                                                                                                                            ||  |||   |||   || || ||||  | |  ||  || |   |   ||  ||| |||  | ||||      ||||| |||||||| ||||||||| | ||||||| ||||||| |||  |||||||||||  | || || ||| |||| || || || ||  |||||||||| |||
gtattttatctaattttgatattattattgaatagtaaattctaatacatattgctgtgaatcaaaaaaactttccagggacaatttttattctcctttacttggattaaagtttctctcgatcatacatgttatgtgtgatctttcaaatgagt--ttatatgttagagtttgtagttactgactcatttaaaatatgcagTTATGAAGGGAGATGTGGCTTGCCTACTAATTTTGATGCTACTTATTGCTATGCTCTGGGTTATGGTGCTGGAGCCCTCCTTCATAGTGGGAAGACTGGA

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|29689204|gb|CB685479.1|CB685479
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|88247475|gb|CI247324.1|CI247324
EST:     GGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAATTATTGCTA
genomic: GGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|88365473|gb|CI680112.1|CI680112
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTG
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTG
EST: gi|29678699|gb|CB674974.1|CB674974
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|29632620|gb|CB637629.1|CB637629
EST:     CATTTCAGAGGCCAATCTCACTTCTTTGA                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: CATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|88369740|gb|CI680411.1|CI680411
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATNGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|88581492|gb|CI698483.1|CI698483
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAA
EST: gi|58687019|gb|CK075706.1|CK075706
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|29689205|gb|CB685480.1|CB685480
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|58684244|gb|CK072931.1|CK072931
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|55431802|gb|CV728921.1|CV728921
EST:     AGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: AGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|33687066|gb|CF315305.1|CF315305
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|58672321|gb|CK061007.1|CK061007
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|428916|gb|D25072.1|D25072
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|8527563|gb|AU092378.1|AU092378
EST:     GCTGAGGGGAAGTACCCCGCNCATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|88578785|gb|CI687736.1|CI687736
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|88197484|gb|CI197186.1|CI197186
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|86854109|gb|CI252100.1|CI252100
EST:     CACATTTCAGAGNCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
genomic: CACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTA
EST: gi|2312262|gb|C28417.1|C28417
EST:     GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGG                         ATATGAAGGAAGATGTGGCCTTCCTACTATTTT
genomic: GCTGAGGGGAAGTACCCCGCACATTTCAGAGGCCAATCTCACTTCTTTGGgtatgtatga ... aattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattttccaaaaaaataattccatctctaatgctgttgctgtgtaattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA
                         ctctaat  putative branch site (score: 3)
     ttccaaaaaaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatgaattgttgcattttccaaaaaaataattccatctctaatgctgttgctgtgtaattttgcagATATGAAGGAAGATGTGGCCTTCCTACTATTTTTGATTCTAACTATTGCTATGCGTTAGGCTACGGTTCTGGGGCACTTCTCCAATGTGGGAAGACAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA