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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCGGGAGGCTTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaatatatatatgttgctctaataagggatttatgcttgttatctctatctgaaaaacactgcttgtacag

Basic information

species Oryza sativa
transcript LOC_Os04g23180.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G065839_T01 (Zea mays), 5'ss of exon 12
TTCCGGGAGGCTTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaatatatatatgttgctctaataagggatttatgctt-gttatctctatctgaaaa-acactgcttgtacag
|||||||| ||| || ||||||||||||||||||| ||  ||||||||||| | ||||||||||||  | ||| ||  ||| |||||   | |||| || |||| | || |    |||||||  |||||||||| ||||
TTCCGGGAAGCTGCAATGTCCAAGGATGATACGGAATTGCTAAGGGTCATGGCCAACTACGgtatgtgaaatacat--gttactctatagatggatctaagctttgctaccatgttctgaaactacactgcttggacag

upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G032293_T02 (Zea mays), 5'ss of exon 4
TTCCGGGAGGCTTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaatatatatatgttgctcta---ataagggatttatgcttg--ttatctctatctgaaaa-acactgcttgtacag
||| |||| ||| || ||||||||||||||||||| ||| ||||||||||| ||||||||||||||  | ||| ||  |||||||||   ||   |||| || ||||   ||| ||  ||||||||  |||||||||  ||||
TTCAGGGAAGCTGCAATGTCCAAGGATGATACGGAATTACTAAGGGTCATGGCTAACTACGgtatgtgaaatacat--gttgctctatagatggtggatataagctttgcttaccttgatctgaaactacactgcttcgacag
















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|88490382|gb|CI427654.1|CI427654
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|14713834|gb|AU197796.1|AU197796
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|88322937|gb|CI548031.1|CI548031
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|88994589|gb|CI117741.1|CI117741
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|8334730|gb|BE039714.1|BE039714
EST:     TTCATTGTCCGAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|88473287|gb|CI410558.1|CI410558
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|58672630|gb|CK061316.1|CK061316
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|29613518|gb|CB618531.1|CB618531
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|86434642|gb|CI105875.1|CI105875
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|4716435|gb|AU057551.1|AU057551
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|9865445|gb|AU101195.1|AU101195
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|88491764|gb|CI429036.1|CI429036
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGTTCATGTCTAACTACG                         GTGAGGATTTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
EST: gi|86494278|gb|CI136911.1|CI136911
EST:     TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACG                         GTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG
genomic: TTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 17 (downstream exon)
Score: 2

TTCCGGGAGGCTTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaata ... gcttgtacagGTGAGGATGTAGTCGAAGCTCTTGGGTATGAAGTGGATCGGCTGGAGTCAGAGATCCAAAAGATTGTGCCTGGGATTAAACATGTTGACATTGAAGCACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCGGGAGGCTTCATTGTCCAAGGATGATACGGAGTTAATAAGGGTCATGTCTAACTACGgtatgcaatatatatatgttgctctaataagggatttatgcttgttatctctatctgaaaaacactgcttgtacag

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