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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagatttatctttttggtaatcaatatagaatcaactcaatgttgcattgttgctcttatttttcgccagctcacttaaaaagcattgtgcatctgga...

Basic information

species Oryza sativa
transcript LOC_Os06g21390.4
intron # 5
splice site 5'
intron type U2

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|88215921|gb|CI215770.1|CI215770
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|29659494|gb|CB655769.1|CB655769
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|218493054|gb|FG951374.1|FG951374
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAAT
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAAT
EST: gi|58687235|gb|CK075922.1|CK075922
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86493358|gb|CI135991.1|CI135991
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86496021|gb|CI138654.1|CI138654
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86492823|gb|CI135456.1|CI135456
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86498369|gb|CI141002.1|CI141002
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|88227716|gb|CI227196.1|CI227196
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|33690378|gb|CF318617.1|CF318617
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTACTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86505484|gb|CI148117.1|CI148117
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|88842871|gb|CI371771.1|CI371771
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|88375844|gb|CI528148.1|CI528148
EST:     AGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: AGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86498945|gb|CI141578.1|CI141578
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86501658|gb|CI144291.1|CI144291
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|89190314|gb|CI392364.1|CI392364
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86485014|gb|CI127647.1|CI127647
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|89181230|gb|CI045313.1|CI045313
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86500831|gb|CI143464.1|CI143464
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|86500426|gb|CI143059.1|CI143059
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
EST: gi|218488371|gb|FG949752.1|FG949752
EST:     TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAAT                         AATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG
genomic: TCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAG

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: 61 (upstream exon), 75 (downstream exon)
Score: 18

GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagattta ... ttcaatgcagAATTATTGAAGTTCGCAGCAGGCCTCCTGGAGGAAGCAATCGTGATCTGAGGACAAGGAAAACAGAAGTTTTGTCGCAAATACGCTCAATAGTCCAAACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATATATGTCAAATgtaagatttatctttttggtaatcaatatagaatcaactcaatgttgcattgttgctcttatttttcgccagctcacttaaaaagcattgtgcatctgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgccagc