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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgcctatctcaccttatttttcacaagtcttatgtatacatgacatttcaaactaatgcaaacttggtctcctttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAATTAATTCAGGATGCATTGTCCGCTTAGCCTAGTAATATTTGGCGCTCTG

Basic information

species Oryza sativa
transcript LOC_Os11g34850.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g34850.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G057056_T02 (Zea mays), 3'ss of exon 3
gttagtgcctatctcaccttatttttcacaagtcttat---gtatacatgacatttcaaactaatgcaaacttggtctcctttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAATTAATTCAGGATGCATTGTCCGCTTAGCCTAGTAATATTTGGCGCT-CTG
|| |||| ||    |||||||| ||      ||||||    || |   |  |  || | || ||||   |||   ||      || ||||||||||||||||||||||||| |||||| | || |||||  |||||||||| |||||||| || ||| ||||  |||||| ||| ||| ||  || || |||
gtcagtgtctcatgcaccttatcttggtt--gtcttacagggtttttgtttccattaatacaaatgtttactacctcattgacttgtgcagGTTGGTTCTAGTGACAGTGTCATGGGGCTGTCAAAGGAGGTTGCAAACAAGTTAATTCACGACGCACTGTCTACTTAGCGTAGCAAT-TTCAGCACTACTG
















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|29683930|gb|CB680205.1|CB680205
EST:     GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG                         GTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
genomic: GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTGgttagtgcct ... ttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
EST: gi|29683870|gb|CB680145.1|CB680145
EST:     GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG                         GTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
genomic: GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTGgttagtgcct ... ttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
EST: gi|88508537|gb|CI436043.1|CI436043
EST:     TTGTTGAAGCAGTG                         GTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
genomic: TTGTTGAAGCAGTGgttagtgcct ... ttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
EST: gi|29683869|gb|CB680144.1|CB680144
EST:     GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG                         GTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
genomic: GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTGgttagtgcct ... ttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
EST: gi|29683929|gb|CB680204.1|CB680204
EST:     GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG                         GTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
genomic: GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTGgttagtgcct ... ttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
EST: gi|88832446|gb|CI019387.1|CI019387
EST:     GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTG                         GTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA
genomic: GTGGCTTGTTGCTTGAACATCCATTGACATTACCATTTGTTGAAGCAGTGgttagtgcct ... ttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgtatacatgacatttcaaactaatgcaaacttggtctcctttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAATTAATTCAGGATGCATTGTCCGCTTAGCCTAGTAATATTTGGCGCTCTG
                      aactaat  putative branch site (score: 2)
                                  cttggtctccttttt  putative PPT
                                            tttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgcctatctcaccttatttttcacaagtcttatgtatacatgacatttcaaactaatgcaaacttggtctcctttttatgcagGTTGGTTCTAGTGACAGTGTAATGGGGATCTCGAAGGATCTTGCAAACAAATTAATTCAGGATGCATTGTCCGCTTAGCCTAGTAATATTTGGCGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG