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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaagtatgctataatttcactgcacaaaaaatgatcctgctgctcacattatcgaagtcagtgatacagtaggacttattttggggggaaatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAAGGAATACACGGCCATCTGCTCATCTTCATGTACATAGATACGAAAAATT

Basic information

species Oryza sativa
transcript LOC_Os01g48270.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g48270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 9
---------aaaagtatgctataatttcactgcacaaaaaatgatcctgctgctcacattatcgaagtcagtgatacagtaggacttattttggggggaaatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAAGGAATACACGGCCATCTGCTCATCTTCATGTACATAGATACGAAAAATT
          ||  | | |||| ||   |||   |||   ||| |        | | |   |  || | | || | |  ||| |||| || |||||| | ||||||||||||||||||||||||| |||||||| |||||||| ||||| |||||  | ||||||||| | || ||||| |||||||||| ||||||||||||||| ||
gaaaaaaacgaatttgtactatgatagtacttttcaatgcatgtta-----atttaaaaagt--aaattattggt-ctttagaactttttctggggg-acatgttgcagAGTTGCCTGAAGTTGGCCCAGTAACTACAGAAGATATTGAACTTGCTTTGAGGAATACAAGACCGTCTGCACATCTTCATGCACATAGATACGAAAAGTT
















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|86260592|gb|CI066465.1|CI066465
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|38480293|gb|CF964382.1|CF964382
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAAC
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAAC
EST: gi|86832493|gb|CI344743.1|CI344743
EST:     AGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86880937|gb|CI339213.1|CI339213
EST:     AAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|163918009|gb|EG715247.1|EG715247
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AATTGCCTGAAGTTGGTCCA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCA
EST: gi|4714792|gb|AU055909.1|AU055909
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86260068|gb|CI065941.1|CI065941
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86434699|gb|CI105932.1|CI105932
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|87021591|gb|CI275990.1|CI275990
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86489964|gb|CI132597.1|CI132597
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|25807028|gb|CA762989.1|CA762989
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86871715|gb|CI331092.1|CI331092
EST:     TCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: TCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86902884|gb|CI312261.1|CI312261
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|87029320|gb|CI250253.1|CI250253
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|11565056|gb|AU165692.1|AU165692
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|117243388|gb|CT843439.1|CT843439
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|58659866|gb|CK048546.1|CK048546
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86413422|gb|CI067827.1|CI067827
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|88832467|gb|CI019408.1|CI019408
EST:     AAGGTTAATGCCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86425638|gb|CI070735.1|CI070735
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86260938|gb|CI066613.1|CI066613
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86498107|gb|CI140740.1|CI140740
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|2428954|gb|C73417.1|C73417
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|88228292|gb|CI227772.1|CI227772
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
EST: gi|86858837|gb|CI275075.1|CI275075
EST:     AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATG                         AGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA
genomic: AAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAA

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: 71 (upstream exon), 30 (downstream exon)
Score: 3

GGCTCTGATATACGCCTTGTGTGCAAGGAGGCGGCAATGCAACCCCTTAGAAGGTTAATGTCGGTTCTTGAAGGAAGGCAAGAAGAAGTGCCTGAGGATGgtacgtgata ... aatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAAGGAATACACGGCCATCTGCTCATCTTCATGTACATAGATACGAAAAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacattatcgaagtcagtgatacagtaggacttattttggggggaaatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAAGGAATACACGGCCATCTGCTCATCTTCATGTACATAGATACGAAAAATT
 tgctcac  putative branch site (score: 3)
                             acttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaagtatgctataatttcactgcacaaaaaatgatcctgctgctcacattatcgaagtcagtgatacagtaggacttattttggggggaaatgttgcagAGTTGCCTGAAGTTGGTCCAGTAACGACAGAAGACATTGAGCTTGCACTAAGGAATACACGGCCATCTGCTCATCTTCATGTACATAGATACGAAAAATT

- -agtatgc
- - - - - - - - - cactgca
- - - - - - - - - - - - -caaaaaa
- - - - - - - - - - - - - - - - - - - tgctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgataca