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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgaatatgaatgacaagtccgttctcatggccaaggcttctaacttaatttattgttcctttgctcacatagccaagctactgttttttattccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGCGGCGATGGTTGTGATGGAGGCTATCCTATCATGGCATGGCGCTACTTTG

Basic information

species Oryza sativa
transcript LOC_Os05g24550.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g24550.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G108849_T01 (Zea mays), 3'ss of exon 5
gtcagtgaatatgaatgacaagtccgttctcatggcc---------aaggcttctaacttaatttattgttcctttgctcacatagccaagctactgttttttattccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGCGGCGATGGTTGTGATGGAGGCTATCCTATCATGGCATGGCGCTACTTTG
|  |||| |||   | ||||   | |||||||| |           ||   || |||    ||   |||| | ||| |||||||| |||||||  ||| |||||   |||| ||| |||||  || || |||||||||||| |||||||||||||||| |||||||||||||| ||||||||||||||||||||   |||||||||||||||||
gcgagtggatacagaagacattgctgttctcatagtttttttaacaaaatattataaaggcatgctttgtcctttttctcacataaccaagctgttgtctttta---cttgcagAGCATTTTACTTTCAGTCAATGACCTACTGGCATGCTGCGGTTTTATGTGCGGCGATGGGTGTGATGGAGGCTATCCTATAGAGGCATGGCGCTACTTTG
















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|29688861|gb|CB685136.1|CB685136
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|58688070|gb|CK076757.1|CK076757
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|27578059|gb|CB000754.1|CB000754
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|29680417|gb|CB676692.1|CB676692
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|29686789|gb|CB683064.1|CB683064
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|33798896|gb|CF325305.1|CF325305
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|58693640|gb|CK082327.1|CK082327
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|33806214|gb|CF328987.1|CF328987
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|29666315|gb|CB662590.1|CB662590
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|29639549|gb|CB644558.1|CB644558
EST:     CATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: CATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|29640250|gb|CB645259.1|CB645259
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|58609130|gb|CK037163.1|CK037163
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|66923450|gb|CX110298.1|CX110298
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
EST: gi|29656220|gb|CB652495.1|CB652495
EST:     TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG                         AACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC
genomic: TTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATGgtcagtgaat ... ttccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatttattgttcctttgctcacatagccaagctactgttttttattccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGCGGCGATGGTTGTGATGGAGGCTATCCTATCATGGCATGGCGCTACTTTG
                tgctcac  putative branch site (score: 2)
                                   ctgttttttattcctt  putative PPT
                                 tactgttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgaatatgaatgacaagtccgttctcatggccaaggcttctaacttaatttattgttcctttgctcacatagccaagctactgttttttattccttgtagAACATTTCGCTATCTGTCAATGACCTAGTGGCATGCTGCGGTTTCATGTGCGGCGATGGTTGTGATGGAGGCTATCCTATCATGGCATGGCGCTACTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG