Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatctttgtggtcaatacagtgatagtttatctttgagtttacttagctaagttttccggcgatgaagcattgatgcatcggccatacgtttctactttctgtcaacaagcaccgtgaaaaaatatggatagtcacatggtgaacttaccattctgattgcaaacttttccccttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAGCCTGAAGGCACAGGCACACCAACAAAAGACTTCAAATCGTTGTTCTCCC

Basic information

species Oryza sativa
transcript LOC_Os03g60740.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g60740.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G068244_T01 (Zea mays), 3'ss of exon 6
gtatgatctttgtggtcaatacagtgatagtttatctttgagtttacttagctaagttttccggcgatgaagcattgatgcatcggccatacgtttctactttctgtcaacaagcaccgtgaaaaaatatggatagtcacatggtgaacttaccattctgattgcaaac----ttttccccttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAGCCTGAAGGCACAGGCACACCAACAAAAGACTTCAAATCGTTGTTCTCCC
                           || | |||  |  |    ||  | |||  |    | |     ||||||      |||    |   |  | ||||    |||  ||||  || |         |||| ||   |||||||| |   |||||||||||  || |    || | | || ||||||||| |||||||| |||||| | ||||||||||||||||||||||| ||||||||||||||    ||||| |||||||| ||||| |   |  |||||||||
--------------------------gta-tatatgctctaaaccacc-atctatatagatctgtctgaaagcatctggttatcatgtacg-gagtatactcatggtc--caaggtccat---------tggacag---catggtgagccagccattctgattttaatcccttttcttctctgataatagGCTCTGCAGTACGAAGAGGCCAAGTTCAAGGCATTTGATTTGGCCTCAAAGCCTGAAGGTGTGGGCACGCCAACAAAGGACTTTAGGGCACTGTTCTCCC
















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|86507768|gb|CI150401.1|CI150401
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|109711615|gb|CI013220.1|CI013220
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|33818134|gb|CF334893.1|CF334893
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAGGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88515532|gb|CI443186.1|CI443186
EST:     CAGACACGAANTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|3762111|gb|C99359.1|C99359
EST:     CAGACACGAA-TCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88490376|gb|CI427648.1|CI427648
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88491906|gb|CI429178.1|CI429178
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88486953|gb|CI424224.1|CI424224
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88472796|gb|CI410067.1|CI410067
EST:     CAAACACGAANTCAATTCCAAGAGCTGATGTTGCTGAAGTTTTTGTTCAG                         GCCCTCCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|89189979|gb|CI013546.1|CI013546
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|33821839|gb|CF336730.1|CF336730
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|3762112|gb|C99360.1|C99360
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88476273|gb|CI413544.1|CI413544
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88847804|gb|CI005990.1|CI005990
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|89198494|gb|CI007554.1|CI007554
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|33817947|gb|CF334802.1|CF334802
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAGGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|117234788|gb|CT847886.1|CT847886
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGC
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGC
EST: gi|88514952|gb|CI442606.1|CI442606
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88289367|gb|CI555729.1|CI555729
EST:     CAGACACGAATTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|86537041|gb|CI177247.1|CI177247
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88239537|gb|CI240014.1|CI240014
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|86506649|gb|CI149282.1|CI149282
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88520427|gb|CI448081.1|CI448081
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|33660166|gb|CF291133.1|CF291133
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88506921|gb|CI434427.1|CI434427
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88441955|gb|CI557608.1|CI557608
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|86507076|gb|CI149709.1|CI149709
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|88227808|gb|CI227288.1|CI227288
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
EST: gi|55415365|gb|CV727741.1|CV727741
EST:     CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAG                         GCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG
genomic: CAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAG

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: 74 (upstream exon), 52 (downstream exon)
Score: 9

CGGGGGAGTGAGGGAGTTGATTGTTGGCAATGACGATGAACTTCTCCAGACAGACACGAAGTCAATTCCAAGAGCTGATGTTGCTGAAGTTTGTGTTCAGgtatgatctt ... cttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAGCCTGAAGGCACAGGCACACCAACAAAAGACTTCAAATCGTTGTTCTCCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagtcacatggtgaacttaccattctgattgcaaacttttccccttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAGCCTGAAGGCACAGGCACACCAACAAAAGACTTCAAATCGTTGTTCTCCC
                                     cttttccccttat  CT-rich tract
                                              ttataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatctttgtggtcaatacagtgatagtttatctttgagtttacttagctaagttttccggcgatgaagcattgatgcatcggccatacgtttctactttctgtcaacaagcaccgtgaaaaaatatggatagtcacatggtgaacttaccattctgattgcaaacttttccccttataatagGCCCTGCAGTATGAAGAGACAAAGTTCAAGGCATTTGATTTGGCTTCAAAGCCTGAAGGCACAGGCACACCAACAAAAGACTTCAAATCGTTGTTCTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG