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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcagattgcttgtttgaatagcaacattgtagctttgacgccataatgccgttgaaactttaccatgtgttatatttggatcgtgattctgatctcaataaacctattgcacacag

Basic information

species Oryza sativa
transcript LOC_Os06g02510.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02510.3 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 5'ss of exon 3
CCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcagattgcttgtttgaatagcaacattgtagct-ttgacgccataatgccgttgaaactttaccatgtgttatatttggatcgtgattctgatctcaataaacctattgcacacag
 || || ||||| || || || ||  |||||||  | || ||||||||||||||||||||   ||| |||||||  || ||||| ||||||||||| |||||   |  ||||  |   ||   |  |||  || ||  | ||  | |  ||  |   || | |    | |   |  | |  |||  || |  |  |  | |  |                  
TCCCACCTCTGGTCCTCTCCGACCTGTTGTTCATGGTCAGACACTTAAGTACAACATGAAAGTTAGAGCTGGAAAAGGATTCACTCTTGAAGAGCTTAAGgt---ttggattcttgaatt---tttcaatgttctaagtgttctctctttatagatattaagatgaaagctcatagt-tgcttgcttctttttgtttttttttag-----------------
















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|86854227|gb|CI254172.1|CI254172
EST:     GGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: GGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|58670768|gb|CK059454.1|CK059454
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|29686267|gb|CB682542.1|CB682542
EST:     GGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: GGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86594633|gb|CI255709.1|CI255709
EST:     GGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: GGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|218504798|gb|FG948126.1|FG948126
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86500579|gb|CI143212.1|CI143212
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|33811788|gb|CF331781.1|CF331781
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86822747|gb|CI251821.1|CI251821
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCGTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|87035705|gb|CI190327.1|CI190327
EST:     GGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: GGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86594654|gb|CI255730.1|CI255730
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|163920526|gb|EG709582.1|EG709582
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|58682724|gb|CK071411.1|CK071411
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86518436|gb|CI158642.1|CI158642
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86498221|gb|CI140854.1|CI140854
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|117233207|gb|CT848039.1|CT848039
EST:     ACAACATGAAGTCTAGAGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|58665756|gb|CK054442.1|CK054442
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|58677962|gb|CK066649.1|CK066649
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86499518|gb|CI142151.1|CI142151
EST:     CTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: CTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|55435028|gb|CV730641.1|CV730641
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86823545|gb|CI256472.1|CI256472
EST:     GGCTTCACCCTTGAAGAGCTGAAG                         GCACCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATTTCAGTGGAT
genomic: GGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|86823022|gb|CI253955.1|CI253955
EST:     TTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: TTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|29686266|gb|CB682541.1|CB682541
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|58595081|gb|CF993389.1|CF993389
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|25801409|gb|CA757370.1|CA757370
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|89165147|gb|CI255204.1|CI255204
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|7212765|gb|D40121.2|D40121
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT
EST: gi|5667631|gb|AU077891.1|AU077891
EST:     ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAG                         GCAGCTGGGATCCCCAAGAAGTTTGCCCCANCCATTGGCATCTCAGTGGAT
genomic: ACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGAT

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: 73 (upstream exon), 75 (downstream exon)
Score: 108

CCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcaga ... ttgcacacagGCAGCTGGGATCCCCAAGAAGTTTGCCCCAACCATTGGCATCTCAGTGGATCACCGCCGTAAGAACCGCTCACTTGAAGGTCTGCAGGCCAATGTCCAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTACTTCTGGACCACTTCGCCCCATTGTTCAGTGCCAAACACTTAAGTACAACATGAAGTCTAGGGCTGGAAGGGGCTTCACCCTTGAAGAGCTGAAGgtaaatcagattgcttgtttgaatagcaacattgtagctttgacgccataatgccgttgaaactttaccatgtgttatatttggatcgtgattctgatctcaataaacctattgcacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG