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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtcctgtttctgctaagttctgtagtgttttcgacatttgatgtaatgtttgcattgactttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG

Basic information

species Oryza sativa
transcript LOC_Os05g49200.2
intron # 5
splice site 3'
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|33795396|gb|CF323568.1|CF323568
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29687282|gb|CB683557.1|CB683557
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|58668482|gb|CK057168.1|CK057168
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|33683538|gb|CF311777.1|CF311777
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|58596651|gb|CK007179.1|CK007179
EST:     ACAATGGCAACCATACATATGTTCCAGTCTCTCACAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29660449|gb|CB656724.1|CB656724
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGA
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGA
EST: gi|125863426|gb|EL586708.1|EL586708
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29675128|gb|CB671403.1|CB671403
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|58658759|gb|CK047439.1|CK047439
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|86908029|gb|CI298797.1|CI298797
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|58668099|gb|CK056785.1|CK056785
EST:     GAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: GAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29657722|gb|CB653997.1|CB653997
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAAGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29660989|gb|CB657264.1|CB657264
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29627821|gb|CB632832.1|CB632832
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|55827430|gb|AU030192.2|AU030192
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29677506|gb|CB673781.1|CB673781
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGA
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGA
EST: gi|218478948|gb|FG952780.1|FG952780
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|218480608|gb|FG959514.1|FG959514
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|58681561|gb|CK070248.1|CK070248
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29636406|gb|CB641415.1|CB641415
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGA
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGA
EST: gi|29644200|gb|CB649207.1|CB649207
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|218495569|gb|FG950148.1|FG950148
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|88396547|gb|CI601030.1|CI601030
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGGGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|86847366|gb|CI286963.1|CI286963
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|33381232|gb|CF196575.1|CF196575
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|218481767|gb|FG945139.1|FG945139
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|218486960|gb|FG945468.1|FG945468
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|218484121|gb|FG947440.1|FG947440
EST:     GGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: GGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|29639939|gb|CB644948.1|CB644948
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|428757|gb|D24912.1|D24912
EST:     ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTNATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
EST: gi|66924030|gb|CX110878.1|CX110878
EST:     ACAAGGGCGACGATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAG                         TTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
genomic: ACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG

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: 69 (upstream exon), 40 (downstream exon)
Score: 219

TGAAGGAGAAGGTGGTGAAATTGTGTTTGGAGGAATGGATCCTAGCCACTACAAGGGCAACCATACATATGTTCCAGTCTCTCAGAAGGGATATTGGCAGgttggtcctg ... ctttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagttctgtagtgttttcgacatttgatgtaatgtttgcattgactttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG
                                       cattgac  putative branch site (score: 219)
                              taatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtcctgtttctgctaagttctgtagtgttttcgacatttgatgtaatgtttgcattgactttgtgcagTTTGAGATGGGCGATGTCCTGATTGGAGGAAAGACCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA