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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactactgaataaccactgctgcccatttataagttcttactgaaacatggtctcattgtcaatacaattggaggaattttttttggggtgctacacataacagaacctaggtaatgttgactccttgtgttatatcaagacagacaaaaagataaatatactctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAAC

Basic information

species Oryza sativa
transcript LOC_Os10g42250.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g42250.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtaactactgaataaccactgctgcccatttataagttcttactgaaacatggtctcattgtcaatacaattggaggaattttttttggggtgctacacataacagaacctaggtaatgttgactccttgtgttatatcaag-acagacaaaaagataaat--atactctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAAC
                                                                              || ||| ||  | |       ||      ||  |  |  | |    |  |  ||  || | ||| ||   |  |    |  ||   || | ||| |||||||  |||||||||| || || |||||||||||| | |||||| |||| ||  |||| |||||||| || || ||||| || ||||||||||  || |||
-----------------------------------------------------------------------------tatgtttattctgctaggtttaatgttttgactcattttttttcctattttcatgccatctaaagcacccgcttatgtgttcatttgtaatatcttgcagTGCTCTGAGGGACCGTCGATTCCCTCCTATACAGGCTAAAGAATTGCCTTACCTGGAATGTACAGTTTCCATTCTGACTGATTATGAAACTGGGCTCAAC
















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|2428016|gb|C72479.1|C72479
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88736026|gb|CI759534.1|CI759534
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|58591535|gb|CF989843.1|CF989843
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATTCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACA
EST: gi|33680238|gb|CF308477.1|CF308477
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|44668540|gb|CR281974.1|CR281974
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|33814577|gb|CF333153.1|CF333153
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|55435942|gb|CV731108.1|CV731108
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|66931214|gb|CX118062.1|CX118062
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88370111|gb|CI585116.1|CI585116
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|58602145|gb|CK012673.1|CK012673
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|55415462|gb|CV727838.1|CV727838
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88417365|gb|CI579026.1|CI579026
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTT-AAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88693360|gb|CI736935.1|CI736935
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAG
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAG
EST: gi|88744786|gb|CI768146.1|CI768146
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88405487|gb|CI588693.1|CI588693
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|218485154|gb|FG948395.1|FG948395
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|33812402|gb|CF332089.1|CF332089
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88417381|gb|CI579042.1|CI579042
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCA-GGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCCTTTCCTCCTATA-AGTCGAAAGAACTGCCGT
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGC-TTTCCTCCTATACAGTCGAAAGAACTGCCGT
EST: gi|58657144|gb|CK045824.1|CK045824
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
EST: gi|88572682|gb|CI664253.1|CI664253
EST:     TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAG                         TGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA
genomic: TTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTA

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: 73 (upstream exon), 70 (downstream exon)
Score: 36

AGAAGGCTACCAATGGTTCAGAACCACGCCTTCGAGGATGCATTGGAACCTTGGAGGCTCGTCAGATTGTCACTGGCTTCAAGGAGTATGCGCTCACAAGgtaactactg ... tctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactccttgtgttatatcaagacagacaaaaagataaatatactctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAAC
 tgttgac  putative branch site (score: 36)
                                          tactctctc  putative PPT
                           acaaaaagataaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactactgaataaccactgctgcccatttataagttcttactgaaacatggtctcattgtcaatacaattggaggaattttttttggggtgctacacataacagaacctaggtaatgttgactccttgtgttatatcaagacagacaaaaagataaatatactctctcgcagTGCATTGAGGGACCGCCGCTTTCCTCCTATACAGTCGAAAGAACTGCCGTATTTGGAGTGTACAGTATCTATACTGACCGAATATGAAACTGCACTTAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG