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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatattattattttccttgcttcatcaaaattaggtattaagagtaaacaaattcaaaaagagaattggctattcttgacataat...

Basic information

species Oryza sativa
transcript LOC_Os07g46790.1
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GRMZM2G136803_T01 (Zea mays), 5'ss of exon 12
GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatattattattttccttgcttcatcaaaattaggtattaagagtaaacaaattcaaaaagagaattggctattcttgacataat-----
||||| |||||||| ||||||||||||||||||||||||||   ||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||||| |    || ||| |   |||   |     | ||   | | | || | ||||   |||  ||  |  | |   | | | | | | |  |     
GACCTCCTTGCACTGAAAGACAAGTACACCACAAGACCAGCGCCAGAGGAAACAATCAATGACCCCACTAACCCAAAGCACTATTGGAGATTCCgtaagtcaatttcc----atcattgtccacctctttatgaaataagacgttttcaataataaaactattttaat-gttactcttcaaatgtcgccttctttttag

upper sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 22
lower sequence: GLYMA19G30580.1 (Glycine max), 5'ss of exon 23
GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatatta-ttattttccttgcttcatcaaa-attaggtattaagagtaaacaaattcaaaaagagaattggctattc-ttgacataat
||| |||| ||| | |||||  | || || ||| | || |||| |||||| |||||||||||||| || || |||||||| ||||||||||||||| ||||        | | | | |||  | |  |   | |||    | ||   |   |   ||   ||| | |  |    | |  ||| ||   ||   | | 
GACTTGCTAGCATTAAAAGAAGAATATACAACACGCCCTGCAACAGAGGAGACAATCAATGACCCTACGAATCCGAAGCACTATTGGAGATTCCgtgagtcttaagcttagtctcagttaactccgctagataatctgttactattgaaccaccttatggaaaattatgatccaagtgtgcttttgactgttgtcag

upper sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 22
lower sequence: AT2G40840.1 (Arabidopsis thaliana), 5'ss of exon 22
GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatattattattttccttgcttcatcaaaattaggtattaagagtaaacaaattcaaaaagagaattggctattcttgacataat
||  || | || || |||||  ||||||| ||  | || |||| |||||| ||||||||||| ||||| ||||| || || || ||||||| ||||||||  ||||      | || ||  |  |   |  |   || |            | || || | ||  ||   |||  ||  | || |  | |||  
GATATGATGGCTCTGAAAGAAGAGTACACTACTCGTCCTGCAACAGAGGAGACAATCAATGATCCAACAAACCCCAAACACTACTGGAGATACCgtaagt--attt------actactaactaacacacaaccctaaga------------actataccagttttaacttaga-ctgttttttgtgcatatag-

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|218488783|gb|FG953776.1|FG953776
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86864928|gb|CI344509.1|CI344509
EST:     AATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88384359|gb|CI551285.1|CI551285
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86899544|gb|CI327446.1|CI327446
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86837005|gb|CI347552.1|CI347552
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTTTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86875507|gb|CI323897.1|CI323897
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86481864|gb|CI124497.1|CI124497
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86879963|gb|CI340014.1|CI340014
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86602648|gb|CI357012.1|CI357012
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86869347|gb|CI339071.1|CI339071
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88263462|gb|CI367236.1|CI367236
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88258937|gb|CI359327.1|CI359327
EST:     GAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: GAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86838937|gb|CI330352.1|CI330352
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86598652|gb|CI355269.1|CI355269
EST:     CAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: CAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|86875630|gb|CI323960.1|CI323960
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|55408542|gb|CV720918.1|CV720918
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88830827|gb|CI079261.1|CI079261
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88253983|gb|CI352609.1|CI352609
EST:     AACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88275409|gb|CI395260.1|CI395260
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88256416|gb|CI358804.1|CI358804
EST:     AACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|89178844|gb|CI391842.1|CI391842
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88509004|gb|CI436510.1|CI436510
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         G
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaag-
EST: gi|88509004|gb|CI436510.1|CI436510
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         G
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaag-
EST: gi|86843610|gb|CI339636.1|CI339636
EST:     AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: AGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
EST: gi|88408409|gb|CI551538.1|CI551538
EST:     TGACCCAACTAACCCGAAGCATTATTGGAGATTCC                         GGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA
genomic: TGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAA

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), 75 (downstream exon)
Score: 85

GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaat ... tttctttaagGGCTACATGTGACATTGGATTCGCTGTTGGACGATAAGGACATCCAAGCAACCATCAAGGAACTTGTCACAAGTAGTGGGAGGTCATTTCCTGGTAAGGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCTGCTTGCACTTAAAGACAAGTACACCACAAGACCAGCAAAAGAGGAAACAATCAATGACCCAACTAACCCGAAGCATTATTGGAGATTCCgtaagtcaattttccaatattattattttccttgcttcatcaaaattaggtattaagagtaaacaaattcaaaaagagaattggctattcttgacataat

- - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga