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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtagcagcagagcacactgttcaagattgatctttttttctgaaacctcatgttgttccgacctgcaacggtgaatcatgagagaactgcatgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGGAAACTTGAAGCAGCTTACCACCTT

Basic information

species Oryza sativa
transcript LOC_Os03g21230.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21230.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G023715_T01 (Zea mays), 3'ss of exon 3
gtatgtagcagcagagcacactgttcaagattgatctttttttctgaaacctcatgttgttccgacctgcaacggtgaatcatgagagaactgcatgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGGAAACTTGAAGCAGCTTACCACCTT
|||||| | | ||   ||| | | | |  |||   ||  | ||         || | ||        || | |  ||  |     |  ||  |   || ||||||||| ||||||| || || || || ||||||||||||||||| | |||||| ||| |||||||||| ||||||||
gtatgtggaatcact-cacccagctaataatta--ctgctcttgcagtttgccacggtga---agtgtgaaccattggcttg---gctaatcgtgcgtgtgcagGGACCTGTCATTCAACAACGAACTCGGCGGCGTGCTCACTCCGACCATCGGGAACCTGAAGCAGCTCACCACCTT
















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|66932156|gb|CX119004.1|CX119004
EST:     AAGGGAGTTCTAGCTGCTGACATAAGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATC
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATC
EST: gi|88431457|gb|CI579574.1|CI579574
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATA
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATA
EST: gi|29672175|gb|CB668450.1|CB668450
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
EST: gi|88407222|gb|CI581309.1|CI581309
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
EST: gi|117246958|gb|CT843762.1|CT843762
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
EST: gi|29674514|gb|CB670789.1|CB670789
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG
EST: gi|88452866|gb|CI574413.1|CI574413
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAA
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAA
EST: gi|88430841|gb|CI571831.1|CI571831
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATCTTGGCGGCGTGC
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGC
EST: gi|58655495|gb|CK044175.1|CK044175
EST:     AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCT                         GGACATGTCATTTAATAAGGATCTTGGAGGCGTGCTCACTCCAAACATCGG
genomic: AAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGG

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: 72 (upstream exon), 75 (downstream exon)
Score: 6

TAAAATTTCTACCATGGGCATCAAGGGAGTTCTAGCTGCTGACATAGGGCAACTGACCGAGCTTCAATCCCTgtatgtagca ... atgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGGAAACTTGAAGCAGCTTACCACCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtagcagcagagcacactgttcaagattgatctttttttctgaaacctcatgttgttccgacctgcaacggtgaatcatgagagaactgcatgtatgcagGGACATGTCATTTAATAAGGATCTTGGCGGCGTGCTCACTCCAAACATCGGAAACTTGAAGCAGCTTACCACCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT