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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttctactcattgctttctgtatggtattcttaggagttacatatacctcccaattctcttgcatttgctatattattgaggtcagcacttgaa...

Basic information

species Oryza sativa
transcript LOC_Os04g56646.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G368908_T02 (Zea mays), 5'ss of exon 7
GAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttctactcattgctttctgtatggtattctta-ggagttacatatacctcccaa-ttctcttgcatttgctatatta-ttgaggtcagcacttgaa
||| ||||| || ||||||||||||||||||||  | || || ||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||| | |     ||      ||      || || |||   ||| | |  ||| |     ||  |    |  |   ||| | ||| ||      || | |    
GAAGGGACTAGATGCAAGGCTCAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTATCATTTGCAGgttagtccctctcttgcaatttgtcaggtgttactctcgtggaatgaactatgcagtaaaagctgaaatataccagctttgttagtttgcagtagtattg---

upper sequence: LOC_Os04g56646.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G061745_T03 (Zea mays), 5'ss of exon 7
GAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttctactcattgctttctgtatggtattctta--ggagttacatatacctcccaatt--ctcttgcatttgctatattattgaggtcagcacttgaa
 || ||||| || |||||||| |||||||||||  | || || |||||||||||||| |||||||||||||||||||| || ||||||||||| ||||||| | | ||  | ||      ||    | |  || | |||  ||| ||  ||  ||    |  |     ||   || | | |  ||  | ||   |||| | |  
AAAGGGACTCGATGCAAGGCTTAGGGAGATCCGAAGCTATTTGGATCTTGTAATTGACGGGAAGCTCCCACTGAATCACGAAATTTTGTACCATTTGCAGgctagtctctttcttgaaatttgtcatgtattacttttactggaattgaatgaactaaacggtaaatgctgaaatctaccagctttcttag--tagcagtag--
















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|86251786|gb|CI018978.1|CI018978
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCGATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88980730|gb|CI022426.1|CI022426
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88438925|gb|CI531105.1|CI531105
EST:     GAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: GAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|89197866|gb|CI013856.1|CI013856
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|58681033|gb|CK069720.1|CK069720
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAA
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAA
EST: gi|88975644|gb|CI021726.1|CI021726
EST:     TTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86487268|gb|CI129901.1|CI129901
EST:     GGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: GGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|29619208|gb|CB624220.1|CB624220
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88509685|gb|CI437191.1|CI437191
EST:     TTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|29619248|gb|CB624260.1|CB624260
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88985211|gb|CI006865.1|CI006865
EST:     TAATTGAAGGGAAGCTCCCACTGAATCGTGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86414901|gb|CI069304.1|CI069304
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88995871|gb|CI037176.1|CI037176
EST:     AATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCGATCTCGATGTAAACGAGCTTATTAAAGCC
genomic: AATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86423679|gb|CI062440.1|CI062440
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86594361|gb|CI251233.1|CI251233
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|94362834|gb|CI052995.1|CI052995
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88695477|gb|CI737515.1|CI737515
EST:     AATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: AATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88245125|gb|CI244974.1|CI244974
EST:     AATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: AATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86903357|gb|CI313720.1|CI313720
EST:     GCTCCCACTGAATCATG-GATTTTGAACCACGTGCA-                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGGTTAGTAAAGCC
genomic: GCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88717102|gb|CI740612.1|CI740612
EST:     AATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: AATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86252997|gb|CI057922.1|CI057922
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86835442|gb|CI347899.1|CI347899
EST:     TTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|89168011|gb|CI109215.1|CI109215
EST:     TGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86876162|gb|CI325628.1|CI325628
EST:     TAAGTGAAGGGAAGCTCCCACTGAATCATGAGAGTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGGTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86873285|gb|CI341510.1|CI341510
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86421022|gb|CI057011.1|CI057011
EST:     ATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: ATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86422198|gb|CI059771.1|CI059771
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88270531|gb|CI385789.1|CI385789
EST:     GTACCACTTGCAC                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: GTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86511450|gb|CI154083.1|CI154083
EST:     ATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: ATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|88263755|gb|CI366656.1|CI366656
EST:     GGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGC
genomic: GGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGT-GTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGC
EST: gi|88958196|gb|CI095715.1|CI095715
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATCTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|86426915|gb|CI072012.1|CI072012
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
EST: gi|29619285|gb|CB624297.1|CB624297
EST:     TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAG                         GATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC
genomic: TAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCC

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: 72 (upstream exon), 58 (downstream exon)
Score: 55

GAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttc ... aaaatcacagGATGTGTTTAATCTGCTCCCCAATCTCAATGTAAACGAGCTTATTAAAGCCTTTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGGACTGGACGCAAGGCTCAGGGAGATCCGTGGGTACTTAGATCTTGTAATTGAAGGGAAGCTCCCACTGAATCATGAGATTTTGTACCACTTGCAGgttcgccttctactcattgctttctgtatggtattcttaggagttacatatacctcccaattctcttgcatttgctatattattgaggtcagcacttgaa

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctccca