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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcattattctttgcttgttttcacaagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcag

Basic information

species Oryza sativa
transcript LOC_Os07g26610.2
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 5'ss of exon 16
lower sequence: GRMZM2G069676_T03 (Zea mays), 5'ss of exon 16
GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcattattctttgctt-gttttcac-aagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggcttt--cttattgctgtatcatgctatatttttactacgcag
|||||||||||| || |||||| | ||||||| |||||| |||||||||||||| |||||   | ||||  | ||||| |||  |||| |||| |||||||||   |||||||||||| ||| |  | ||  |||| |||| ||||||||  ||  |  |||||||  |  |   ||||||  ||   ||||||  | |  ||| | |||              
GTCCTTCCGTGACTATGGAGAATCCGTCTTGAGACATTTAGAGAATGCAATCAGCAAAGACCCAAATCTCCGTAAAGCCCCGGTGAACCATGAGGGCgtatgtacatattctttgctttgttctttcgaaacttgaatatagatcttgatgcat--aatttttcttctgcgagaaagctggatttctgcttatt-ttatggcataccatacacag---------
















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|89183519|gb|CI046084.1|CI046084
EST:     GAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: GAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86831683|gb|CI301533.1|CI301533
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86259591|gb|CI065464.1|CI065464
EST:     TGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGTTTATCCCTCCAT
genomic: TGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|218504169|gb|FG954519.1|FG954519
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|88268519|gb|CI378454.1|CI378454
EST:     AAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: AAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|87008287|gb|CI301045.1|CI301045
EST:     TAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: TAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|29660679|gb|CB656954.1|CB656954
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|89186475|gb|CI048147.1|CI048147
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86426061|gb|CI071158.1|CI071158
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86892585|gb|CI312008.1|CI312008
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86258642|gb|CI064995.1|CI064995
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcattattctttgcttgttttcacaagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC