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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattattaaataatttgagacatcttctttttgtctgggtgtaactataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA

Basic information

species Oryza sativa
transcript LOC_Os04g45070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G122937_T01 (Zea mays), 3'ss of exon 2
gtgattattaaataatttgagacatcttctttttgtctgggtgtaactataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA
|| |||||| |||||||   |      || |   |  || ||  || | | ||||| | ||| | |||  ||   | ||||| | |||||||||||||||||||| |||||||||||||| ||||||||||| ||||| || ||||||||||||||||||||||||||
gtaattattgaataattgttg----tgtcatcgagattgagtacaagt-tgccaattaaaacctgaaacatggtctgcagATCTCGCTCTTGCAAGGGTGGAAACAGAGAAGAGGAACTCTTTGATCAAAGCTTGGGAAGAGAATGAGAAGACAAAAGCTGAGAACAA

upper sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116538_T02 (Zea mays), 3'ss of exon 2
gtgattattaaataatt--tgagacatcttctttttgtc-tgggtgtaactataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA
|| |||||| |||||||       ||||    ||  ||| || ||  |||||| |  || | ||| | |||  ||   | ||||| | |||||||||||||||||||| ||||||||||||||  |||| ||||||||||| || ||||||||| |||||||||| |||||
gtaattattgaataattgtcttatcatcgagattgagtcatgtgtacaactatgcacattaaaacttgaaacatgatctgcagATCTCGCTCTTGCAAGGGTGGAAACGGAGAAGAGGAACTCTCTGATTAAAGCATGGGAAGATAATGAGAAGGCAAAAGCTGATAACAA

upper sequence: LOC_Os04g45070.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G45820.1 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtgattattaaataatttgagacatcttctttttgtctgggt---gtaact-ataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA
              |   ||   |  |      ||  |||||  |  ||  ||   |||| | |   |||        |    ||       |||||||    |||||     ||||||  |||||||  |  ||||| |||||||||||||| || | ||||||| |||| |||||||||| 
gtcagctgataacaacactttgtttctcatgtccagtttcttagttacttagttcagtaatttacttcaaatgtgtgttgtgtgtgtttggtcagATGTGATACTTGCCGACTTGGAAAAAGAGAAGAAAACGTCATTCATCAAAGCATGGGAAGAGAGTGAGAAGTCAAAGGCTGAGAACAG

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|86884366|gb|CI310950.1|CI310950
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGA
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGA
EST: gi|38471757|gb|CF955888.1|CF955888
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88311646|gb|CI574863.1|CI574863
EST:     AGATGAAACTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88975844|gb|CI024095.1|CI024095
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|50878545|gb|AF527706.1|AF527706
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|87010775|gb|CI312467.1|CI312467
EST:     GGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCANAG
genomic: GGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|87026567|gb|CI252521.1|CI252521
EST:     TGCTCAAGGGGGCTCTAATGGCAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: TGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|58693172|gb|CK081859.1|CK081859
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|29684469|gb|CB680744.1|CB680744
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|89167373|gb|CI252904.1|CI252904
EST:     CTGCTCAAGGGGGCTCTAATGGCAGAG                         ATGTTGCTCTTCCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: CTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|29670320|gb|CB666595.1|CB666595
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|38470437|gb|CF954568.1|CF954568
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88404224|gb|CI575712.1|CI575712
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88741665|gb|CI765173.1|CI765173
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|38471661|gb|CF955792.1|CF955792
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88445327|gb|CI587221.1|CI587221
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|87005481|gb|CI285703.1|CI285703
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|86478310|gb|CI120943.1|CI120943
EST:     GAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTCCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: GAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|29670321|gb|CB666596.1|CB666596
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|313084059|gb|HO213842.1|HO213842
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|89165064|gb|CI255121.1|CI255121
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88367239|gb|CI564003.1|CI564003
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|58601478|gb|CK012006.1|CK012006
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88406404|gb|CI596531.1|CI596531
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAG
EST: gi|88405645|gb|CI598925.1|CI598925
EST:     AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAG                         ATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAA
genomic: AGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAA

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: 511

AGGTTGCAGATGAACCTCCTGCCGAGAAACCTGCTCAAGGGGGCTCTAATGACAGAGgtgattatta ... tgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctttttgtctgggtgtaactataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA
                           caataac  putative branch site (score: 511)
                  taactata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattattaaataatttgagacatcttctttttgtctgggtgtaactataccaataacaacgtaaaagttgccatccagATGTTGCTCTTGCAAGGGTGGAAACTGAGAAGAGGAACTCATTGATCAAAGCATGGGAGGAAAATGAGAAGACAAAAGCTGAGAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA