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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacaccacgtcatcacttcttgtcctactaaagatcaattacttgagatgctagaatgtttcaagatattctaatttccaccaccaattgaaaaa...

Basic information

species Oryza sativa
transcript LOC_Os12g40550.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G130034_T01 (Zea mays), 5'ss of exon 11
AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacaccacgtcatcacttcttgtcctactaaagatcaattac-ttgagatgctagaatgtttcaagatattctaatttccaccaccaattgaaaaa
| |||||||||||||||||||||||||||| ||||||||||||  || | |||  | ||      |    | |   || | ||   |     || || || |||      | ||  |  || |   |    |  ||     |
AGTATCACCAATGGGTATGATCTTCATTCCCTGTTACAAAGgttcgtgctccattttattttcgatcactcaaaataatagcatgcatgcctaggtgtta-aatagaaatacatcctagaaatattatgttcctttaggtga

upper sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA20G34790.1 (Glycine max), 5'ss of exon 11
AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacaccacgtcatcacttcttgtcctactaaagatcaattacttgagatgctagaatgtttc----aagatattctaatttccaccaccaattgaaaaa
  | || |||||||| ||||| ||||||||||||||||||||| | |||    | |  |    | |   | |       ||    | | ||  ||  ||||     |     || | ||| ||| |  |||||   |||||||| 
GCTGTCTCCAATGGGCATGATTTTCATTCCATGTTACAAAGgtatttac--tgcttttttgtgtgtgtgcatgtgtgctatgtgct-cgtgcaatagtagagctccttctataataaattttaagtatcaccagtgattgaaaa-

upper sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA10G32850.2 (Glycine max), 5'ss of exon 10
AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtac-accacgtcatcacttcttgtcctactaaagatcaattacttgagatgctagaatgtttcaagatattctaatttccaccaccaattgaaaaa-
  | || |||||||| ||||| ||||||||||||||||||||| | |||  |  | |  |   |   |||     |       |  | ||  | |||  | |        ||  ||| |       |  |  |    ||| | 
GTTGTCTCCAATGGGCATGATTTTCATTCCATGTTACAAAGgtatttactgctgctttttttttgtgtgtgtgtgtgtgtgctatgtgctcta-atgtgacaccaccatcag-cattgtttgcgtaattaatagccaaaagaa

upper sequence: LOC_Os12g40550.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv05s0020g04900.t01 (Vitis vinifera), 5'ss of exon 11
AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacaccacgtcatcacttcttgtc-ctactaaagatcaattacttgagatgctagaatgtttcaagatattctaatttc-caccaccaattgaaaaa----
|||||| |||||||||||||| ||||||||||||||||||||| ||  |      ||||| ||  |||   | ||| ||  ||  || | | |  |  || |   | |  | ||  |  |||    ||  |    ||    |     
AATATCTCCAATGGGTATGATATTCATTCCATGTTACAAAGgtatgagc----tatcatctctctttgctacaactgaaattc--tttcataaccttttataccatgtttaaattatggaatgaagcatgattggtttctgattgca

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|29673191|gb|CB669466.1|CB669466
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|29639192|gb|CB644201.1|CB644201
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|29676280|gb|CB672555.1|CB672555
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|58684218|gb|CK072905.1|CK072905
EST:     AATATCACCAATGGGTATGATCTTCATTCCAGGGTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|66923480|gb|CX110328.1|CX110328
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAAC
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAAC
EST: gi|88517619|gb|CI445273.1|CI445273
EST:     AATATCACCAATGGGTATGATGTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|29665068|gb|CB661343.1|CB661343
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88245424|gb|CI245273.1|CI245273
EST:     CACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: CACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|14980959|gb|BI305637.1|BI305637
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAAC
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAG-CCCGAAGAATATGCGTCACCAGAGGACATGGCGAAC
EST: gi|55410334|gb|CV722710.1|CV722710
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88542548|gb|CI471885.1|CI471885
EST:     AATATCACCAATGGGTATGATGTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGGGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|86896323|gb|CI330185.1|CI330185
EST:     AATATCACCAATTGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88265593|gb|CI376495.1|CI376495
EST:     TGGCCAGAATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: TGGCCAGAATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|86887402|gb|CI313305.1|CI313305
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88518252|gb|CI445906.1|CI445906
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGGCGAAC
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACAT-GGCGAAC
EST: gi|3760122|gb|C97380.1|C97380
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|38471018|gb|CF955149.1|CF955149
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88525555|gb|CI452561.1|CI452561
EST:     AATATCACCCATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAGGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|86887413|gb|CI313316.1|CI313316
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88552168|gb|CI482297.1|CI482297
EST:     ATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: ATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88990252|gb|CI107678.1|CI107678
EST:     AATATCACCCATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|29625973|gb|CB630984.1|CB630984
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|27578088|gb|CB000783.1|CB000783
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88265802|gb|CI376704.1|CI376704
EST:     AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGCCGAACG
genomic: AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
EST: gi|88365913|gb|CI545772.1|CI545772
EST:     TGATCTTCATTCCATGTTACAAAG                         GTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG
genomic: TGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACG

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: 67 (upstream exon), 55 (downstream exon)
Score: 7

AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacac ... ctggttgcagGTTACAGCCACAAGCCCGAAGAATATGCGTCACCAGAGGACATGGCGAACGGTGTGAAGGTGCTTGCCTTGGCAATGGCCAGATTATCCCTGCAGTGAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATATCACCAATGGGTATGATCTTCATTCCATGTTACAAAGgtctgtacaccacgtcatcacttcttgtcctactaaagatcaattacttgagatgctagaatgtttcaagatattctaatttccaccaccaattgaaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccacc