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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttattcttgtttcacatgtttagacaagttactttggcacatatattatataacaatgtatggattcaactgccagtgtgaccacacaattcttt...

Basic information

species Oryza sativa
transcript LOC_Os04g39270.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G169516_T05 (Zea mays), 5'ss of exon 7
GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttattcttgtttcacatgtttagacaagttactttggcacat-atattatataa-caatgtatggattcaactgccagtg-tgaccacacaattcttt
|| ||||| ||||| |||||||||||||| |||||||| |||||||| |||||||||||||||||||||||||| ||||||||| | || |||||  ||   |||| ||   || |  |  |   | |||  | ||||    | | |  |||  |   || |   | | ||    || |   
GTTCATGACGAAAGAGAAATGGACCGTGTTTTAGGGATTGATGGTGTACAGCTCATCGGCATCAATAACCGTAATCTCGgtatgctgtttttgttgaact--tttacactgatttcaattcctagtgataccagataagtcttttgtctattttatcacctgaaatcagcagtggatccag-

upper sequence: LOC_Os04g39270.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G48220.3 (Arabidopsis thaliana), 5'ss of exon 8
GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttattcttgtttcacatgtttagacaagttactttggcacatatattatataacaatgtatggattcaactgccagtgtgaccacacaattcttt
|| ||||| |||||||| ||||| |||||  | |  || || || ||| ||||||| |||||||||||||||||||| ||||    || ||||   || |  |      ||| ||      || ||   |  |    |  | |||    |   ||  |||                   
GTCCATGACGAAAGGGAGATGGATCGTGTTCTTGCAATTGAAGGAGTCGAGCTCATTGGCATCAATAACCGTAACCTTGgtaa---atgcttgaaccagacctcctttaaagctagacataca-atccttcttgatccgttttatcaccttttctttcag-------------------
















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|29616383|gb|CB621395.1|CB621395
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAA
EST: gi|4714825|gb|AU055942.1|AU055942
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|23513963|gb|BU673400.1|BU673400
EST:     GTTAGGGATAGATGGTGTC-AGCTCATCGGCATCAATA-CCGTAAACTCG                         AGA-TTTT-AAGTTGATATT
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATT
EST: gi|29616384|gb|CB621396.1|CB621396
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|4714826|gb|AU055943.1|AU055943
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATANCCGTANCCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|88986358|gb|CI033589.1|CI033589
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|29663297|gb|CB659572.1|CB659572
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|86849316|gb|CI297783.1|CI297783
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|30226600|gb|CB964492.1|CB964492
EST:     GTAAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGGAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
EST: gi|29615583|gb|CB620595.1|CB620595
EST:     GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCG                         AGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA
genomic: GTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAA

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: 69 (upstream exon), 62 (downstream exon)
Score: 17

GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttatt ... attattgcagAGACTTTTCAAGTTGATATTTCAAACACTAAAAATCTTCTTGAGGGTGAAAGAGGACAAACTATAGCTCAGAAAGGCATAATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCATGATGAAAGGGAAATGGACCGTGTGTTAGGGATAGATGGTGTCCAGCTCATCGGCATCAATAACCGTAACCTCGgtatgttattcttgtttcacatgtttagacaagttactttggcacatatattatataacaatgtatggattcaactgccagtgtgaccacacaattcttt

- - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA