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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTCTTGCTGGGCATCAAACATGGGTCTGGTGAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacgagatcggatccattgcgttgtgcttttgcgtgatcagtggcctgtgagttttgtgttttgcttccgggcttctggcggcgtactggtgcc...

Basic information

species Oryza sativa
transcript LOC_Os06g37180.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 2
GTTGCTCTTGCTGGGCATCAAACATGGGTCTGGTGAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacgag--atcggatccattgcgttgtgcttttgcgtgatcagtggcctgtgagtt-ttgtgttttgcttccgggcttctggcggcgtactggtgcc---
             |   |  | |||||||||||||||||| |||| || |    |||||||||| ||||| ||||||||||||||||||| |||||  |   ||||||    | |   || | | |||  |  | | || ||  |  |  || |     |    |  |   |    |||| | |||    
-------------GTTGTTCAGCATGGGTCTGGTGAAGGAAGGCGTCGACA---TGGAGGAGGGAACCCTAGAGATCGGCATGGgtgagtcacgagcgacgagatcca---agctcgcctatagtgtgcgccttaggctttgtttcgtcatgatggatgtgtcagtgt---gtactgtaccgatgcatca

upper sequence: LOC_Os06g37180.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 2
GTTGCTCTTGCTGGGCATCAAACATGGGTCTGGTGAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacgag--atcggatccattgcgttgtgcttttgcgtgatcagtggcctgtgagttttgtgttttgcttccgggcttctggcg----gcgtactggtgcc---
             |   |  | |||||| ||||||||||| |||  || |    |||||||||| ||||| ||||||||||||||||||| || ||  |   ||||||         |||   |||   | | |     |   |||| || |||  | |    |||  ||  |    || || |  | ||   
-------------GTTTTTCAGCATGGGCCTGGTGAAGGAAGGCATCGACA---TGGAGGAGGGAACCCTTGAGATCGGCATGGgtgagttactagcgacgagatccaa--------gctcgcgcgcagt-attccttaggatgtttagtatttatcctttcagctgttgatgtgtcgcatagtcataccgat
















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|55410497|gb|CV722873.1|CV722873
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29633929|gb|CB638938.1|CB638938
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29641774|gb|CB646781.1|CB646781
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29631355|gb|CB636364.1|CB636364
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29683215|gb|CB679490.1|CB679490
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29630856|gb|CB635865.1|CB635865
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29617703|gb|CB622715.1|CB622715
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29675287|gb|CB671562.1|CB671562
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29669854|gb|CB666129.1|CB666129
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29630446|gb|CB635455.1|CB635455
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29681069|gb|CB677344.1|CB677344
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
EST: gi|29642143|gb|CB647150.1|CB647150
EST:     GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGG                         AGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG
genomic: GAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAG

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), 54 (downstream exon)
Score: 214

GTTGCTCTTGCTGGGCATCAAACATGGGTCTGGTGAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacg ... caatttgcagAGTACAGGACTGTTTCTGGTGTGGCAGGACCTCTGGTTATCTTGGATAAAGTAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTCTTGCTGGGCATCAAACATGGGTCTGGTGAAGGATGGCGCCGCCGATTTGGAGGAGGGGACCCTGGAGATCGGCATGGgtgagtaacgagatcggatccattgcgttgtgcttttgcgtgatcagtggcctgtgagttttgtgttttgcttccgggcttctggcggcgtactggtgcc

- - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcggcg