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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGAAGATGCTGGTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgcatgattctttttaccttctttttgtataattgacatggtctgaaatacagtgcattgtgaagtatatccgtataacctcttgctttatataaaaaatatttaattcag

Basic information

species Oryza sativa
transcript LOC_Os01g51220.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G439457_T01 (Zea mays), 5'ss of exon 4
GCTGGAAGATGCTGGTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgcatgattctttttaccttctttttgtataattgacatggtctgaaatacagtgcattgtgaagtatatccgtataacctcttgctttatataaaaaatatttaattcag--
|||||| |||||||||||||||||||||||||| || |||||||||||||||||||| ||||||||||||| |  | || ||| |      |  || || ||| |   | ||   ||||||         || |  | ||   |||   |||    |||  | | || || ||  | |||   
GCTGGAGGATGCTGGTTATGCTGTTGGTGCAAGGGTGCTTGAACTACTCTGTCACAGGGAGAAGgtttgataccagtttgtttgt-----ttggttatacaatggtttttgt--aaaatac---------tggaaca-atttttatg--ctccatttttgcaaataatattttgtagtcatat
















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|88382318|gb|CI633176.1|CI633176
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATCCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88303013|gb|CI668859.1|CI668859
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88347620|gb|CI634305.1|CI634305
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGACAGACTCGACTGCCAGGTATATTATCGTTCACTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88336811|gb|CI644238.1|CI644238
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGANTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88356314|gb|CI652718.1|CI652718
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88338206|gb|CI633325.1|CI633325
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88575096|gb|CI666865.1|CI666865
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88305183|gb|CI651980.1|CI651980
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|109974426|gb|DT806902.1|DT806902
EST:     GTTATGCTGCTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGGTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88575793|gb|CI669938.1|CI669938
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATCCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|163929185|gb|EG713058.1|EG713058
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88719072|gb|CI742582.1|CI742582
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATCATCGTTCAT
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCAT
EST: gi|88381600|gb|CI682265.1|CI682265
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88327973|gb|CI648377.1|CI648377
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAG
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAG
EST: gi|88308467|gb|CI650876.1|CI650876
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC

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: 64 (upstream exon), 75 (downstream exon)
Score: 35

GCTGGAAGATGCTGGTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGAAGATGCTGGTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgcatgattctttttaccttctttttgtataattgacatggtctgaaatacagtgcattgtgaagtatatccgtataacctcttgctttatataaaaaatatttaattcag

- - - - - - - -  ATGCTG
- - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - GCAAGA