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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagtagatcgtttgcttctcttgttttttctcatcatgtattttgtttaggaaaataatctttactttctacattactgcatttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTC

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G006507_T02 (Zea mays), 3'ss of exon 3
gtgaagtagatcgtttgcttctcttgttttttctcatcatgtattttgtttaggaaaataatctttactttctacattactgcatttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTC
||  | | |  |  |||| ||| ||||||||  |  |||| |  ||  |||||  ||         |    |||    | ||    || ||||||||||||||||| ||||| || |||||||| ||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||||||   ||
gtagattcgcacacttgcctctattgtttttctttctcatatgcttgctttagagaaggggga---aaacactaatcgaatgtggctcacagCTTCACTTCCCTTCGAGTATCATATCCTATATTGAAGACAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G119725_T02 (Zea mays), 3'ss of exon 3
gtgaagtagatcgtttgcttctcttgttttttctcatcatgtattttgtttaggaaaataatctttactttctacattactgcatttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTC
|| || |    |  |||| ||||||||||||     |||| || ||  |||||  ||         |    ||||  || ||    | |||||||||||||||||| ||||| ||||| ||||| |||||||||||||||||||||||||||||||||||||| || ||||| ||||||||||||||   ||
gtaaattgacacacttgcctctcttgtttttgtgtctcatatacttgctttagagaaggggga---aaacactactctaatgtggcttgcagCTTCACTTCCCTTCGAGTATCATCTCTTATATCGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTGAACCATGCTTGGGCATCTGCAAACAATC
















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|88396973|gb|CI578122.1|CI578122
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTAAAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTA
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTA
EST: gi|29646523|gb|CB651530.1|CB651530
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58608259|gb|CK036292.1|CK036292
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAG
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAG
EST: gi|58669315|gb|CK058001.1|CK058001
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|29673248|gb|CB669523.1|CB669523
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58659150|gb|CK047830.1|CK047830
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|29641723|gb|CB646730.1|CB646730
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|88728131|gb|CI751641.1|CI751641
EST:     TGTCGGGATACTTGTNTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTNACTTCCCTTCCAGTATTATCTCCTATATA
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATA
EST: gi|29673598|gb|CB669873.1|CB669873
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|29616238|gb|CB621250.1|CB621250
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|88356602|gb|CI626217.1|CI626217
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAG
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAG
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58666569|gb|CK055255.1|CK055255
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58690262|gb|CK078949.1|CK078949
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58687148|gb|CK075835.1|CK075835
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58680355|gb|CK069042.1|CK069042
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAG
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAG
EST: gi|58601351|gb|CK011879.1|CK011879
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
EST: gi|58605686|gb|CK033719.1|CK033719
EST:     TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAG                         CTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC
genomic: TGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGC

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: 71 (upstream exon), 75 (downstream exon)
Score: 16

AAGATCAAATGAGGGGATGAGGCTCATATTCTCGGCAGTTGTTGGTGTTATGTTGGGATACTTGTTTGGGGTTTCCTTCCCTACAGTAAATATAACCAAGgtgaagtaga ... catttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtattttgtttaggaaaataatctttactttctacattactgcatttcgcagCTTCACTTCCCTTCCAGTATTATCTCCTATATAGAAGATAGGAACTCTGGCATCACAACCCAGACATTGTTAAATCATGCGTGGGCATCTGCAAATCGTC
                 aaaataatctttactt  TA-rich tract