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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTTGTTGAGTTGGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaatggagctttcgtgtcagtcttttcttccctatgtatttgcctaccattctaaatatgcatttatgacactctttttttctttttaccag

Basic information

species Oryza sativa
transcript LOC_Os04g46620.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G039263_T02 (Zea mays), 5'ss of exon 2
GTTCTTGTTGAGTTGGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaatggagctttcgtgtcagtcttttcttccctatgtatttgcctaccattctaaatatgcatttatgacactct--ttttttctttttaccag
||||||||||||||||||||||| |||||  | ||||| ||||||||||| || || ||||| || ||||| ||||| || || |||||||| |      |  ||    |||   |||||     | || |||  ||||||  | |  |  ||||  |     |      ||||||||| ||  |||
GTTCTTGTTGAGTTGGCTGAGCTCCAAGATCGTGAGGTAGGAGATGGAACTACTTCCGTTGTCATCATAGCGGCAGAGTTACTCAAGgtaatta------gtctt----tcacctttttcactattgtgaattaccctacctgttttcagctgcacgtgcactaacaagattttttcttattgtcag

upper sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G110626_T01 (Zea mays), 5'ss of exon 4
GTTCTTGTTGAGTTGGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaatggagctttcgtgtcagtcttttcttccctatgtatttgcctacca--ttctaaatatgcattta-tgacactctttt-tttctttttaccag
|||||||||||||||||||| || |||||| | ||||| ||||||||||| || || ||||| || ||||| |||||  |||| |||||||| ||           |  ||  | || ||     | || |||  ||| |||  ||  | ||   |||  | | ||||   ||| |||||| ||  |||
GTTCTTGTTGAGTTGGCTGAACTCCAAGACCGTGAGGTAGGAGATGGAACAACTTCCGTTGTCATCATAGCGGCAGAGCTGCTCAAGgtaattaa----------tgcttcgcttttctcgctattgtgaattgcccttccagttttcagatgcacatgcactaacaccgatttgtttcttattgtcag

upper sequence: LOC_Os04g46620.1 (Oryza sativa), 5'ss of exon 4
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTCTTGTTGAGTTGGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgt-aatgaaatggagctttcgtgtcagtcttttcttccctatgt----atttgcctaccattctaaatatgcatttatgac--actctttttttctttttaccag---
|||||||| ||||| ||||| |||||||| ||||| || || ||||| || ||||||||||| ||  |||| || || ||| | ||||| | |   ||     |||  | |   | |  | ||||    ||    |  |   |  |||  ||| |||   || ||||   |    | || | | | ||   |   
GTTCTTGTCGAGTTAGCTGAACTTCAAGATAGAGAAGTCGGTGATGGGACTACATCTGTTGTTATTGTAGCTGCTGAGTTGTTGAAGgttagtttgattactgttttctttggttttggttttcctagagttgggagatttttcacatggtaactattgcttgatgattaatgggtcttatgtatatatttgcag

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|88729236|gb|CI752746.1|CI752746
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAAC
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAAC
EST: gi|88389824|gb|CI626593.1|CI626593
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88576618|gb|CI670763.1|CI670763
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACA
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACA
EST: gi|86826131|gb|CI311004.1|CI311004
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88358293|gb|CI606802.1|CI606802
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCT
EST: gi|88334889|gb|CI648664.1|CI648664
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAANAAAATCCATCCGACA
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACA
EST: gi|88395151|gb|CI609467.1|CI609467
EST:     TGGGACATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCA-TGATCTTGTGAGAAACAAAATCCATCCGACGTCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88372614|gb|CI610937.1|CI610937
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTA
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTA
EST: gi|13807435|gb|AU181953.1|AU181953
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88424401|gb|CI607987.1|CI607987
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCT
EST: gi|88301610|gb|CI597303.1|CI597303
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88350316|gb|CI623254.1|CI623254
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACAT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACAT
EST: gi|88396969|gb|CI578118.1|CI578118
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGAAGAATTGCTAAAG                         CGGGGCAATGATC
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATC
EST: gi|58663765|gb|CK052451.1|CK052451
EST:     TGGGTGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88416925|gb|CI573640.1|CI573640
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAC                         CGGGGCCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAG
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGC-AATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAG
EST: gi|88426602|gb|CI579431.1|CI579431
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACA
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACA
EST: gi|88315088|gb|CI610147.1|CI610147
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATC
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATC
EST: gi|58682634|gb|CK071321.1|CK071321
EST:     TGGGTGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88727997|gb|CI751507.1|CI751507
EST:     TGGGAGATGGAACGACATCTGTCGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAATTC-ATCGGACATTTATTA
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTA
EST: gi|88354225|gb|CI637791.1|CI637791
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCT
EST: gi|58690688|gb|CK079375.1|CK079375
EST:     TGGGTGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|29682947|gb|CB679222.1|CB679222
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|58653426|gb|CK042106.1|CK042106
EST:     TGGGTGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGT
EST: gi|88336708|gb|CI643883.1|CI643883
EST:     TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAG                         CGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTA
genomic: TGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTA

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), 60 (downstream exon)
Score: 58

GTTCTTGTTGAGTTGGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaat ... tttttaccagCGGGGCAATGATCTTGTGAGAAACAAAATCCATCCGACATCTATTATCAGTGGCTACAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTTGTTGAGTTGGCTGAGCTTCAAGACAGAGAGGTGGGAGATGGAACGACATCTGTTGTGATAATAGCCGCAGAATTGCTAAAGgtaatgaaatggagctttcgtgtcagtcttttcttccctatgtatttgcctaccattctaaatatgcatttatgacactctttttttctttttaccag

- - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - GATGGA