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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 14
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag
|||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| || ||||||||||||   ||||    ||||           ||||||| |    | | |  || || |   ||| ||    |   || ||  ||||
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAGgtatgc--aagcagacaggtta----------cattagtaaacactgttggtacagtgtacacca-actgtctttgactttctgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G126453_T02 (Zea mays), 5'ss of exon 8
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatg-atccatacaaaatgcaacatttggcag
|||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||||||||   ||||     |||   ||||         || |    |   | ||| ||||  | | |       |   || ||  ||||
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgc--aagcacacaagtttacttta---------gtaaccactaccggcacagtatataccaactttttttttgactttctgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G435582_T01 (Zea mays), 5'ss of exon 3
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattg-tcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag
|||||||| ||||| ||||| |||||||| | |||||||||| |||||||||||||||| || || |||||||| |||||||||||||||   ||||     |||   |||| |  ||| ||  |    | |   |  |    |  |   |      |   || ||  ||||
TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgc--aagcacacaagtttactttagtaatcactaccggcacagtatataccaacttctttttt------tttgactttctgcag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G354532_T01 (Zea mays), 5'ss of exon 2
---------TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatcca--tacaaaatgcaacatttggcag
         |||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||||||||   ||||     |||   ||||         || |    |   | ||| ||||   |||  | |    |   || ||  | ||
GCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAGgtatgc--aagcacacaagtttacttta---------gtaaccactaccggcacagtatataccaacttctttttttgactttctggag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA17G13850.1 (Glycine max), 5'ss of exon 21
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgc---ttgagcatgtgggttg-gttttattg--tcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag
|||||||| || || ||||||||||| ||||||||||||||  | || ||||||||  | || || ||||||||  ||||||||||| ||   || | || | |  ||| ||| |||||  |||||    ||   |||  |  |  | || | ||                      
TGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttttaaccaagggtattgtgttgtattgattcattgaatataactttactagc--tttgtttcag---------------------

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 22
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag------------------
|||||||| ||||||||||| ||||| |||||||| || ||  |||| || ||||| |||||||| ||||| ||  |||| ||||| ||||| | |||||   |||  |||||  || || |   ||   ||  |  |  |||  |  |||  |  |  || | ||   ||                  
TGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAGgt-tgctttatcatgtcatttg--tttatattcctttgaagttctctt--ttcctttattttaaatattatttttaatactttttagaattcatatgagccattt

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GLYMA05G03270.1 (Glycine max), 5'ss of exon 19
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgc--ttgagcatgtgggt-tggttttattgtcattagt--gatttatttggtcacggtatgatccatacaaaatgcaacatttggcag
|||||||| || || ||||||||||| ||||||||||||||  | || ||||||||  | || || ||||||||  ||||||||||| ||  || | | |  |||| | ||||| |  | |||  |  ||| ||  |   |  | | || | ||                      
TGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAGgtaagccttttaacttaagggtattgttttgtattgattcattggatgtaactttactagctttgtttcag---------------------

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 5'ss of exon 22
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgct--tgagcatgtgggttggttttattgtc-----atta--gtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag
|||||||| || |||||||| || || |||||||||||||| ||||||||||| |||||||||||||| || ||  ||||||||||||| |  |   | |   |    | | |  |  |     ||||  ||   || ||   ||    |||  |    ||   || ||| |||  | ||
TGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAGgtatgttgctagacgttaagaacagctctcatacctgtttattacagttcctttttctttctgaatatcttttgaacgggat-caaaattatgtag

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 23
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 22
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgct---tgagcatgtgggttggtttt--attgtcattagtgatttatttggtcacggtatga-tccatacaaaatgcaacatttggcag------------------------------------------------------------------------------------------
|||||||| ||||||||||||||||| |||||||| |||||  |||| |||||||| || || || ||| | ||  |||| |||||| | |   | |   | |   ||  |     | | |   ||     ||  |   ||    ||||  |||||  |    |  ||  |                                                                                                
TGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAGgtaagttgaataaatctttaaattcatccacaacttttgctataatgttcctcactctttttatgggtccatggatttagtgacggtaactgttcaatccttttaattcgccattctgatctttagtttctttcttcttttcctgttaaaaaatttattgttaacttagatttattgtttcag

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|58684670|gb|CK073357.1|CK073357
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
EST: gi|58691499|gb|CK080186.1|CK080186
EST:     -TTTCTCATTA-CAAGT-AAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
EST: gi|58692889|gb|CK081576.1|CK081576
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGC
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGC
EST: gi|58607816|gb|CK035849.1|CK035849
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
EST: gi|163926070|gb|EG715026.1|EG715026
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
EST: gi|218497816|gb|FG965087.1|FG965087
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
EST: gi|66922707|gb|CX109555.1|CX109555
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
EST: gi|86831749|gb|CI301599.1|CI301599
EST:     TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG                         GTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG
genomic: TTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATG

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), 70 (downstream exon)
Score: 43

TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttga ... catttggcagGTTGATAGTATGCTAGGAAGGAGAGAGAATCCAGGGGAGCATGAAGCGATGCGCAAGATGAAAAACGAATTTATGGTGAATTGGGATGGATTACGCACTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAGgtatgcttgagcatgtgggttggttttattgtcattagtgatttatttggtcacggtatgatccatacaaaatgcaacatttggcag

- - - - - - - - - - - - - - - - - - - - - - AGCAAG