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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactcttgccatgtcctggccgactgtttccctgtctttggttcagtaggaaaccatgcactaacgattatgttttatttgtgggggccatgacag

Basic information

species Oryza sativa
transcript LOC_Os02g08300.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G143462_T01 (Zea mays), 5'ss of exon 12
ATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTA-TTTAAACCCGgtgagaactcttgccatgtcctggccgactgtttccct----gtctttggttcagtaggaaaccatgcactaacgattatgttttatttgtgggggccatgacag-----------------------------
 | ||||||||||| ||||| || ||||||||| | || |||||||| || || ||||| ||||||| ||| ||||||||   || | || |||  |  ||||||||||||| || ||   ||||  |  |     |||     | | |||   ||| |   ||  ||   | |      | |||| ||  |  |  || || |                               
-TTGAAGCATTCTTAGCCTGCGATAGGAACGAGGAGCTAGCAGCAAACTATCTCCTTGAGCATGCTGGTGAGGAAGATTAAGCGGGAGTAGTTTTCATACGgtgagaactct-gctatcctctggttggttaccctccttaacatatatggca-agtggctcactgtggggtgatttcctttttttcttcttttgaaccttgcctctcgtcgacatctgaccgacattgatcaag

upper sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G143462_T03 (Zea mays), 5'ss of exon 12
ATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTA-TTTAAACCCGgtgagaactcttgccatgtcctggccgactgtttccct----gtctttggttcagtaggaaaccatgcactaacgattatgttttatttgtgggggccatgacag----------------------------------------
 | ||||||||||| ||||| || ||||||||| | || |||||||| || || ||||| ||||||| ||| ||||||||   || | || |||  |  ||||||||||||| || ||   ||||  |  |     |||     | | |||   ||| |   ||  ||   | |      | |||| ||  |  |  || || |                                          
-TTGAAGCATTCTTAGCCTGCGATAGGAACGAGGAGCTAGCAGCAAACTATCTCCTTGAGCATGCTGGTGAGGAAGATTAAGCGGGAGTAGTTTTCATACGgtgagaactct-gctatcctctggttggttaccctccttaacatatatggca-agtggctcactgtggggtgatttcctttttttcttcttttgaaccttgcctctcgtcgacatctgaccgacattgatcaagattttttttag
















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|88967884|gb|CI098126.1|CI098126
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|40486995|gb|BX898244.1|BX898244
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTGGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88261283|gb|CI364859.1|CI364859
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CGTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88554521|gb|CI484707.1|CI484707
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|86871825|gb|CI331997.1|CI331997
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88976735|gb|CI257507.1|CI257507
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|89168138|gb|CI109342.1|CI109342
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88276832|gb|CI395995.1|CI395995
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88266856|gb|CI368632.1|CI368632
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGC
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88267177|gb|CI379112.1|CI379112
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|86503859|gb|CI146492.1|CI146492
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88838256|gb|CI373616.1|CI373616
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88831799|gb|CI369481.1|CI369481
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|89178685|gb|CI391683.1|CI391683
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|86490040|gb|CI132673.1|CI132673
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88980844|gb|CI022534.1|CI022534
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88975027|gb|CI023278.1|CI023278
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88966384|gb|CI119519.1|CI119519
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88991630|gb|CI019808.1|CI019808
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|27547445|gb|CA765529.2|CA765529
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTGGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|86833994|gb|CI340133.1|CI340133
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|86490031|gb|CI132664.1|CI132664
EST:     CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: CCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
EST: gi|88380349|gb|CI518719.1|CI518719
EST:     AACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCG                         CTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG
genomic: AACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGG

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), 72 (downstream exon)
Score: 12

ATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactc ... gccatgacagCTTATTCTGTACACCTGCCCTGCAATTTATCAGACTTTTGAAGTTTGCGGGTGCTTTGGATCCAAATTGAACAAGCTGAGATGGAGCTAACACCGCGTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGAAGCATTCTTCGCCTGTGACAGGAACGAGCAACTCGCAGCAAATTACCTTCTTGAACATGCTGCTGATGAAGATTAGATGGAATTATTTAAACCCGgtgagaactcttgccatgtcctggccgactgtttccctgtctttggttcagtaggaaaccatgcactaacgattatgttttatttgtgggggccatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA