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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaatatctgatcataatgttattgttgggtttacttcaattggttatattccatttcttatacaattga...

Basic information

species Oryza sativa
transcript LOC_Os02g32030.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32030.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AC203173.3_FGT004 (Zea mays), 5'ss of exon 1
CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaatatctgatcataatgttattgttgggtttacttcaatt--ggttatattccatttcttatacaattga----
         |||||||||||||| |  |||||||||||    ||||||||||| ||||| ||||| ||||||||||| || ||||||||||||||||| |||||||  || || |    |   | ||    |  ||| |  || |  |  |||| ||| |  |  ||   ||     | |||| | |||   ||      ||    
---------ATGGTGAAGTTCACGGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAATATGTCTGTTATTGCTCATGTGGACCATGgtatgt-tcaaaaca---ctactttgttagatgttatatagtcct--taatatttttgagcctctttgtttttaaaatttatttcgttttcaatgtttaagagcta

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G113250_T01 (Zea mays), 5'ss of exon 2
CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaatatctgatcataatgtt---attgttgggtttacttcaattggttatattccatttcttatacaattga-
  |||||||||||||||||||||||  |||||||||||    ||||||||||| ||||| ||||| ||||| ||||| || ||||||||||||||||| |||| ||  ||||| |  |      |   | || || ||  ||  |  ||||   ||  ||  | ||  | |  ||  | || | ||  | ||| ||    ||  
GGAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGTGCCATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTTATTGCTCATGTGGACCATGgtaggt-tcagaaca-ctgcccaagacattttgatgtc-aattgttctgtttcaatatttaagctttgtactgttcttgat-tgccgatgcttctattcatgct

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G095851_T01 (Zea mays), 5'ss of exon 2
CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaatatctgatcataatgttattgttgggtttacttcaattggttatattccattt-cttatacaattga---
  |||||||||||||||||||||||  ||||||||||||   ||||||||||| ||||| ||||| ||||| ||||| |||||||||||||||||||| |||||||  ||||| | |  |   | |  |||  |||  ||       |    || |   |  |  ||    ||  || | |  |||| ||   | | ||||   
GAAGTCAAGATGGTGAAGTTCACAGCTGAAGAGCTCCGCGCTATCATGGACAAAAAGAACAACATTCGTAACATGTCTGTCATTGCTCATGTGGACCATGgtatgt-tcagaacactgctctgtagcatatatatacatgcattgcttaacgttttcaagccttttta---tgtgtagacttaatttgctccaatatttgagct

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S138_93V6.1 (Physcomitrella patens), 5'ss of exon 2
CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaata-tctgatcataatg-ttattgttgggtttacttcaattggttatattccatttcttatacaattga--
            ||||||||  | |  || |||||||||   ||||||||||||||| | |||||| | || ||||||||||| || ||||| || ||||||||||  |  | |   | |  || |     |  || ||||    |  ||  ||  ||| |  ||  |  | |  |  ||  ||              ||||  
------------GTGAAGTTTTCGGCGGACGAGCTCCGCGCCATCATGGACAAGAAGCACAACATCAGGAACATGTCCGTCATCGCCCATGTCGATCACGgtatgt--cgaagtccctgtctcttgcagtgtggtagtctgggtctggtgactagggtttgagtt--tgtagtgtgcgatgatcggaagggcgactgcttgaaa

upper sequence: LOC_Os02g32030.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ28367 (Selaginella moellendorffii), 5'ss of exon 2
CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaatatctgatcataatgttattgttgggtttacttcaattggttatattccatttcttatacaattga
            ||||| ||||| | ||||||||| ||||||||||||||||||||| | |||||||| || ||||| || ||||||||||| || ||||||  ||  |       || |  |       | | || || |  |    ||   | |    ||| |  ||                               
------------GTGAAATTCACGGCAGAAGAGCTGCGCCGGATCATGGACAAGAAGCACAACATCCGGAACATGTCTGTGATTGCTCATGTCGATCACGgtgagtttcttctagatttt--ccatccattcagtagctaa--agctcgtcgatctgaaattttcgccag------------------------------

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|88444119|gb|CI594492.1|CI594492
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58588787|gb|CF987095.1|CF987095
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGGGCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|88731919|gb|CI753326.1|CI753326
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58593699|gb|CF992007.1|CF992007
EST:     CAAGAAGAATAACATCCGTAATATGTCCGGGATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58672167|gb|CK060853.1|CK060853
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|88395529|gb|CI613051.1|CI613051
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|117217683|gb|CT845087.1|CT845087
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58591626|gb|CF989934.1|CF989934
EST:     CAAGAAGAATAACATCCGTAATATGTCCGGGATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58605041|gb|CK033074.1|CK033074
EST:     ACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: ACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|287209|gb|D16013.1|D16013
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58605540|gb|CK033573.1|CK033573
EST:     GCTCATGTGGA-CACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: GCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58608952|gb|CK036985.1|CK036985
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|88693181|gb|CI736756.1|CI736756
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|88411944|gb|CI566673.1|CI566673
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|4879124|gb|AU063423.1|AU063423
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|27554053|gb|CA997953.1|CA997953
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58682939|gb|CK071626.1|CK071626
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|58674100|gb|CK062786.1|CK062786
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
EST: gi|5667333|gb|AU077575.1|AU077575
EST:     CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACG                         GAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC
genomic: CAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCC

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: 75 (upstream exon), 75 (downstream exon)
Score: 153

CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgcca ... ctctctgcagGAAAGTCTACACTTACGGATTCTCTTGTGGCGGCTGCTGGTATTATTGCCCAGGAAGTTGCGGGTGATGTTCGCATGACTGATACCCGTGCAGATGAAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTAGTCAAGATGGTGAAGTTCACAGTAGAAGAGCTCCGCCGGATCATGGACAAGAAGAATAACATCCGTAATATGTCCGTCATTGCTCATGTGGACCACGgtatgtgccagaatagttatgactggtgtattaatatctgatcataatgttattgttgggtttacttcaattggttatattccatttcttatacaattga

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG