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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatgtgctttaagaaatacacaagttaaaacacattggccaatcctatgtctttctattccattgcagtaaggtcctcttgaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTTGAAGTTTACAAGGAAGGCTTGGCGCAACTGC

Basic information

species Oryza sativa
transcript LOC_Os11g01420.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01420.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G467086_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------------tattatgtgctttaagaaatacacaagttaaaacacattggccaatcctatgtctttctattccattgcagtaaggtcctcttgaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTTGAAGTTTACAAGGAAGGCTTGGCGCAACTGC
                                                                                       ||   | |  | |    | |  ||  |  ||   |||    |  ||  |||   |||||||||||||| | | || |   |||  || ||| | ||||||||| |||||||||| || ||||| |||||||| || |||||||| || || |||||    |||||||||||||||||||| |||||||||  ||| ||  
gtacagtattactgtgtgatggctgttatatgtttgattttgaagatatgccataattcattatgtaacttatgattaatctaaagttaggctctattgtgctcagtttacgtgaaaatcgacacctactcattttatccttttctattccattgtattgag-tatccttcgatctctctcttgcagCGGCTGCTTGGGATACAAATGGCGACATTCCGTCTATACCTTGTGTGTCGCTGGTCGGGCGATGACTTTGAAGTTTACAAAGAAGGCTTGATGCACCTAG
















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|3759048|gb|C96747.1|C96747
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88503749|gb|CI431255.1|CI431255
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|27548175|gb|CA767467.2|CA767467
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|55440810|gb|CV733717.1|CV733717
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTTTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|86525962|gb|CI166168.1|CI166168
EST:     ACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: ACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88459689|gb|CI521949.1|CI521949
EST:     TTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|86526028|gb|CI166234.1|CI166234
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88662749|gb|CI473698.1|CI473698
EST:     AGTAATNTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTN                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: AGT-ATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|66915344|gb|CX102192.1|CX102192
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG

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: 68 (upstream exon), 67 (downstream exon)
Score: 23

GGGCGGTGGAATTAGTTGCAGATCACATAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtacatactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTTGAAGTTTACAAGGAAGGCTTGGCGCAACTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctatgtctttctattccattgcagtaaggtcctcttgaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTTGAAGTTTACAAGGAAGGCTTGGCGCAACTGC
                                         tttctgt  CT-rich tract
         tttctatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatgtgctttaagaaatacacaagttaaaacacattggccaatcctatgtctttctattccattgcagtaaggtcctcttgaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTTGAAGTTTACAAGGAAGGCTTGGCGCAACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- -tatgtgc
- - - - - - - - - - acacaag
- - - - - - - - - - - - - - -aaaacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcttgaa