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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGTATCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAACAGAGAGAAGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcacttgctattcttcaagttaatttcttataaagttggaacttcacccctaatgttggaacaactgaataagtgcttccttccttccttatga...

Basic information

species Oryza sativa
transcript LOC_Os01g62420.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 5
CAAGGTATCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAACAGAGAGAAGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcacttgctattcttcaagttaatttcttataaagttggaacttcacccctaatgttggaacaactgaataagtgcttccttccttccttatga---
|||||| |||||||||||||||||||||||||||||||||| |||||||| ||||||||||| ||||| |||||||| || ||||| || |||||||| ||||| ||     | | | |||   ||||  |||| || |  ||     || | |  || |  ||   |   | | ||   | |||      | | ||||    
CAAGGTCTCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAGCAGAGAGAGGCAGGAACAACAATGGATGTTGTTGCTGCACAAACAAAGGCTATTGCTGgtaacttttacagttttacttgctgttatattctgatcatcttatgtttttaact-tattcctgcttctgttcagtatagggttcagg--atgcatatgctct

upper sequence: LOC_Os01g62420.3 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv13s0019g01090.t01 (Vitis vinifera), 5'ss of exon 5
CAAGGTATCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAACAGAGAGAAGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgta---atttcact--tgctattc---ttcaagtt---aatttctta--taaagttggaacttcacc----------cctaatgttg-gaacaactgaataagt--gcttccttccttccttatga------------------------------------------
 ||||  | ||||| || |||||  |||| ||||| ||||| ||| ||||| | ||| |||| |||||||||||||| || ||||| ||||| ||||||||||   ||| ||||     ||| |   | ||  ||   | ||| | |  |   | |  || ||| |             ||||| |  |||   || ||| |||   | | ||||     ||                                              
AAAGGCCTTAAGGTGATAGCTTGTGTTGGAGAGACTCTTGAGCAGCGAGAATCTGGATCAACTATGGAAGTTGTTGCTGCACAAACAAAAGCAATTGCAGgtatccattccactaccattatccgcatgcagttttacagtttttcaattggtgctacaagttctctgtctattgtatttaatgctctgaaatgctaaattagttaacatgcttcaaggattgcattaagttcctcttttgactgtttcaaatttatttctattccag
















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|33693438|gb|CF321677.1|CF321677
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692149|gb|CF320388.1|CF320388
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|29669431|gb|CB665706.1|CB665706
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33694018|gb|CF322257.1|CF322257
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33689964|gb|CF318203.1|CF318203
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
EST: gi|27576926|gb|CA999620.1|CA999620
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33828594|gb|CF340117.1|CF340117
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCANACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33827559|gb|CF339596.1|CF339596
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|58679577|gb|CK068264.1|CK068264
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692177|gb|CF320416.1|CF320416
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692251|gb|CF320490.1|CF320490
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33685938|gb|CF314177.1|CF314177
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33689283|gb|CF317522.1|CF317522
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTAGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|163928335|gb|EG712603.1|EG712603
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGC--ATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33687151|gb|CF315390.1|CF315390
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGGTTGTTTTGGCATATGAACCAGTTTGG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATG-TTGTTTTGGCATATGAACCAGTTTGG
EST: gi|58683989|gb|CK072676.1|CK072676
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAG
EST: gi|33692942|gb|CF321181.1|CF321181
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33828383|gb|CF340010.1|CF340010
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCANACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33691808|gb|CF320047.1|CF320047
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGAC
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGAC
EST: gi|58669404|gb|CK058090.1|CK058090
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33689638|gb|CF317877.1|CF317877
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCATACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACC
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACC
EST: gi|33691551|gb|CF319790.1|CF319790
EST:     GCAGGAACAACGATGTGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAACGATG-GAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33693863|gb|CF322102.1|CF322102
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33685357|gb|CF313596.1|CF313596
EST:     GCAGGAACAACGATGGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAACGATGG-AAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33801873|gb|CF326808.1|CF326808
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33692386|gb|CF320625.1|CF320625
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGA
EST: gi|33691552|gb|CF319791.1|CF319791
EST:     GCAGGAACAACCGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGAC
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGAC
EST: gi|33690870|gb|CF319109.1|CF319109
EST:     GCAGGAACAACNGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
genomic: GCAGGAACAAC-GATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATG
EST: gi|27576424|gb|CA999118.1|CA999118
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|58674808|gb|CK063495.1|CK063495
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33690114|gb|CF318353.1|CF318353
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG

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: 74 (upstream exon), 70 (downstream exon)
Score: 55

CAAGGTATCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAACAGAGAGAAGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGTATCAAGGTAATTGCTTGCATTGGTGAGACCCTTGAACAGAGAGAAGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcacttgctattcttcaagttaatttcttataaagttggaacttcacccctaatgttggaacaactgaataagtgcttccttccttccttatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG