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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgtagctctcccatgagtctgctattattcttcaatgaaattacagtcaccttttagtttgttgtcacttgatttcttcccacaccacccaat...

Basic information

species Oryza sativa
transcript LOC_Os07g43060.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43060.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G086805_T02 (Zea mays), 5'ss of exon 2
AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgtagctctcccatg----agtctgctattattcttcaatgaaattacagtcacctt-ttagtttgttgtcacttgatttcttcccacaccacccaat
||| |||||  ||||||| ||  ||||||| ||||| || |||||||||||||||||||||     | ||| |  ||     | | || |  |  || ||| |     | || ||   || |   ||| || || ||  | || |     |     |    
AATTATCTCTCTGATGGACCCCAGTAGGAGCTGGGCAGCCCGTTGGTTGAGAATTGgtgagccttgatctcccgtatcctgcaatttgtttgtcctcctcagtctg-ctgcattcgttttgtcttttttttttctctccacttatgtaagctgtgtc----
















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|88212631|gb|CI212271.1|CI212271
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCTCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|55431292|gb|CV728660.1|CV728660
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|55431294|gb|CV728661.1|CV728661
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88838475|gb|CI375023.1|CI375023
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88380030|gb|CI513620.1|CI513620
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88976243|gb|CI024460.1|CI024460
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|163919996|gb|EG709802.1|EG709802
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTCGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88382569|gb|CI535777.1|CI535777
EST:     CTCCGTGATGAATCCTGGTAGGANTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88376412|gb|CI535516.1|CI535516
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTTTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|87019382|gb|CI279892.1|CI279892
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|86530402|gb|CI170608.1|CI170608
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|86423375|gb|CI060948.1|CI060948
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|58610018|gb|CK038051.1|CK038051
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|11610378|gb|AU166054.1|AU166054
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|8857385|gb|AU094703.1|AU094703
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|163928022|gb|EG709470.1|EG709470
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|88833830|gb|CI077311.1|CI077311
EST:     CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: CTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
EST: gi|33684821|gb|CF313060.1|CF313060
EST:     TAGGAGTTGGGCTGCTCGTTGGTTGAGAATTG                         GGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG
genomic: TAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGG

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: 56 (upstream exon), 59 (downstream exon)
Score: 22

AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgt ... caatctgcagGGAAGTTCATCCCTGGGTGCTATACGCTGGCTGTCGCGGAGGAGCTTCCGGAGGAGTACCAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATAATCTCCGTGATGGATCCTGGTAGGAGTTGGGCTGCTCGTTGGTTGAGAATTGgtgagtacgtagctctcccatgagtctgctattattcttcaatgaaattacagtcaccttttagtttgttgtcacttgatttcttcccacaccacccaat

- - - - - - GATGGA
- - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccacc