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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtccatttagttaattgacagttttgttgctagtgcaaactactatttggtactaaaattgagttctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA

Basic information

species Oryza sativa
transcript LOC_Os02g05340.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 9
gtatggtccatt-tagttaattgacagttttgttgctagtgcaaactactatttggtactaaaattgagttctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
||||| |   |  |  ||   | | |   |  ||  | |    |    || |||  | || |   | || ||| || |||  | ||||||| || ||||||||||| || ||||||||||| |||||||| || || || || || |||||||||||||| || |||||||||||||| |||||||| |
gtatgtttgttagtcattggctcataagctctttttttgcattagaacctttttctttctca---taagctct-tttttgctt-tacagCCCAGGATGCTTTTAACTGTCGATGAGGATCTGAAGCCCCTCTCAGTACCTGTCCGCGTTGGGCAAGCTGTGGACGTGGTTGGTCAGGCAGGAAGGCCTA

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 23
lower sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 22
gtatggtccatt-tagttaattgacagttttgttgc-tagtgcaaactactatttggtactaaaattgagt--------tctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
||||| |   |  |   |    | || ||   |||  | | | | || ||| ||  | ||||   ||||          | | || | |  ||||||||| || |||||||| || || || |||||||| |||||||| || || || || || || |||||||| || || |||||||||||||| |||||||| |
gtatgtttgttagtcactgccagccacttcgattgggtggagtagacaactgtt--ggactatggttgaaccatctttcttttttttcgcttgtacagCCCAGGATGCTTTTGACTGTCGACGAGGATCTGAAGCCCCTGTCAGTACCTGTCCGCGTCGGGCAAGCGGTCGACGTGGTTGGTCAGGCAGGAAGGCCGA

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 23
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 23
----------gtatggtccatttagttaattgacagttt-----tgttgctagtgcaaactactatttggtactaaaattgagttctcttcttgtatg-tacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
             | |  || ||  ||  |  ||| |||       ||  |  |   | ||  | |||  |  ||   || | || ||| |||  ||| ||||||| |||||| |  | || ||||||||||||||||| || || ||||| || |||||||| || || ||||| ||||| ||||| ||||||||  |||| |
gttaattctaaatttgagcacttcatttctctacaatttgtgaccatttgtttttggatcttgtgtttattcttactgtt-atttatctactttgatgctacagCCAAGAATGTTGATGACTGTGGATGAGGATCTAAAACCTCTGTCTGTACCTGTACGGGTGGGTCAGGCTGTGGATGTTGTTGGACAGGCTGGTCGGCCAA

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 23
lower sequence: PP1S3_553V6.1 (Physcomitrella patens), 3'ss of exon 23
-------------------------------------------------------------------------------------------------------gtatggtccat--ttagttaattgacagttttgt-tgctagtgcaaactactatttggtactaaaattgagttctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
                                                                                                       || | |||  |  ||  ||  ||  | | ||  | | ||  |  ||| ||   |||  || ||| ||||   | | || ||| ||| ||||||  | ||| |  ||||  |||||||  || |||| ||  |  ||||||| ||||| ||||| ||||||||||||||||||||||| |||||  | ||||
gtaaatctttcagtttcatcttgtagacacttaaatgctgaaagtttgatgtcatggtgaattgctagtgtagcttctaaattcggcaatctgaataatcctagtctcgtctttctttttttgtttctctgcttgctcttctctttgaaattatggttt--tattaacattg---tttgttattggatg-acagCCACGGATGTTGATAACTTTGGATGAAAATTTAAAACCTTTGCCTGTTCCTGTACGAGTTGGTCAAGCTGTTGATGTGGTTGGTCAAGCTGGTCGCCCCA

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|88381509|gb|CI682165.1|CI682165
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|38471464|gb|CF955595.1|CF955595
EST:     TTCTAGGGAAATACCACTACATTCTTTACATGATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|29671492|gb|CB667767.1|CB667767
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86478402|gb|CI121035.1|CI121035
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|58681607|gb|CK070294.1|CK070294
EST:     GGGAAATACCACTACATTC-TTACATTATCGTCTTGGCGATGCAG                         CCTA-AATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: GGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|29667415|gb|CB663690.1|CB663690
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86481455|gb|CI124088.1|CI124088
EST:     CTACATTCTTTACATGATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: CTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86597729|gb|CI274720.1|CI274720
EST:     GGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: GGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|29626310|gb|CB631321.1|CB631321
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|87017868|gb|CI273890.1|CI273890
EST:     GAAATACCACTACATTCTGTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: GAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86513311|gb|CI155944.1|CI155944
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86521408|gb|CI161614.1|CI161614
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|87040544|gb|CI195166.1|CI195166
EST:     AATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: AATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|87016365|gb|CI271776.1|CI271776
EST:     AAATACCACTACATTCTGTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: AAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|88582162|gb|CI699549.1|CI699549
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGG
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGG
EST: gi|86437495|gb|CI119217.1|CI119217
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86520198|gb|CI160404.1|CI160404
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86437677|gb|CI119597.1|CI119597
EST:     CCACTACATTCTTGACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTGTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: CCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|87036016|gb|CI190638.1|CI190638
EST:     ATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: ATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|38471736|gb|CF955867.1|CF955867
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|88580987|gb|CI697953.1|CI697953
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTA
EST: gi|86596990|gb|CI270786.1|CI270786
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|88369867|gb|CI680543.1|CI680543
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGA
EST: gi|86479268|gb|CI121901.1|CI121901
EST:     TTCTAGGGAAATACCACTACATTCTTGACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|66922910|gb|CX109758.1|CX109758
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
EST: gi|86437636|gb|CI119358.1|CI119358
EST:     TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAG                         CCTAGAATGTTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA
genomic: TTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCA

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: 75 (upstream exon), 73 (downstream exon)
Score: 50

TGGAGGCCTTGTTACTGTATTGCATGCTTGCCTCGATATGAAATCCACCATTCTAGGGAAATACCACTACATTCTTTACATTATCGTCTTGGCGATGCAGgtatggtcca ... gtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagtgcaaactactatttggtactaaaattgagttctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA
                      tactaaa  putative branch site (score: 50)
                                   ttctcttcttgtat  putative PPT
                      tactaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggtccatttagttaattgacagttttgttgctagtgcaaactactatttggtactaaaattgagttctcttcttgtatgtacagCCTAGAATGCTTTTAACGGTGGATGAGGATCTAAAGCCCCTATCTGTTCCAGTACGGGTTGGGCAAGCTGTTGATGTGGTTGGTCAGGCTGGAAGGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG