Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatactagctgttgtgatcttgtagacttgcattttattgacctataattttgaaaattggtatgtttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT

Basic information

species Oryza sativa
transcript LOC_Os04g36050.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G147916_T01 (Zea mays), 3'ss of exon 3
gtatgatactagctgttgtg-atcttgtagacttgcat---tttattgacctataattttgaaaattg-gtatgtttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT
||| | ||||| ||   ||  ||     |   || |||   ||||| | |   |  |||||||  ||| ||||||        ||||| ||||| | ||||| |||||||||||||||||||| || ||||| |||||||| |||||||| ||||| |||||  |||||||||| |  ||| | |
gtaggctactaactacagtacattaaacattatttcatgcatttatggtctatttcttttgaattttgtgtatgtactgttacagGCTCTCAAGCATAATGGCTCTTTGTATGCTCATGTTTACTTCGCCCGTTCGGGTTATCCTGTGGACCCTACAGATCCAAAATATGAGCAGAAATCTTCGT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G016894_T01 (Zea mays), 3'ss of exon 2
gtatgatactagctgttgtgatcttgtagact----tgcattttattgacctataattttgaaaattggtatgttt-ctgcc-tagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCC-GCTCGGG-TTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT
||| | ||||| |||  || |  ||  | | |          ||  ||  ||||   ||| ||| || || | | | |||    ||||| ||||| | ||||| |||||||||||||||||||| || |||| | ||||| ||| |||||||| ||||| ||||| ||||||||||| |  ||| |  
gtaggctactaactgcagtaacattaaacattatttcatgcatttatggtctatttcttttaaattttgtgtatgtactgttacagGCTCTCAAGCATAATGGCTCTTTGTATGCTCATGTTTACTTCGCCCCGTTCGGGGTTATCCTGTGGACCCTACAGATCCAGAATATGAGCAGAAATCTTC--

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G462387_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------------------------------gtatgatactagctgttgtgatcttgtagacttgcattttat-------tgacctataattttgaaaattggtatgttt-ctgcc-tagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT---------
                                                                 ||   || |||    ||    |    || || |  |||| ||       || |||||   |||  || || || | ||| ||     | ||||| ||| | | ||  ||||||| | | |||||||| |||||| ||||||||||||||||||| |  || |||||||| ||||| || |  |||  ||         
gtaaacataccatatgcagtataggaagttaccagcactcacaataattaacatactatccttcagtgctatgctactaatttcagtaacataaacat-tatttcatgcaactatggcctatttgttttgaattttgtgtatttactattacatgctattaagCATATTGCATCTTTGTTTCCCCATGTTTACTTTGCCAGCTCGGGTTACCCTGTGGACCTAACAGATCCTGAGTATGATCACAAGTCTATATTTGGGAGGA

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G437119_T02 (Zea mays), 3'ss of exon 2
gtatgatactagctgttgtgatcttgtagact--tgcattttatt--gacctataattttgaaaattggtatgttt-ctgcc-tagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT
||| | |||||  ||  || |  ||    | |  | |||   | |  |  ||||   |||  || || || ||||| |||    ||||| ||||| | ||||| |||||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||||||||||| |  |||||||
gtaggctactaattgcagtaacatttaccattatttcatgcaactatggtctatttgttttgaattttgtgtgttttctgttacagGCTCTCAAGCATAATGGATCTTTGTATGCTCATGTTTACTTTGCCCGCTCGGGTTACCCTGTGGACCCAACAGATCCTGAATATGAGCAGAAATCTGCAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G848529_T01 (Zea mays), 3'ss of exon 2
gtatgatactagctgttgtgatct---tgtagacttgcattttattgacctataattttgaaaattggtatgttt-ctgcc-tagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT
||| | ||||| ||   ||    |     |    |      ||  ||| ||||   |||  || || || | | | |||    ||||| ||||| | ||||| |||||||||||||||||||| || ||||| |||||||| |||||||| ||||| |||||  |||||||||| |  ||| | |
gtaggctactaactacagtacattaaacattatttcatgcatttatgatctatttcttttgaattttgtgtatgtactgttacagGCTCTCAAGCATAATGGCTCTTTGTATGCTCATGTTTACTTCGCCCGTTCGGGTTATCCTGTGGACCCTACAGATCCAAAATATGAGCAGAAATCTTCGT

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|58607128|gb|CK035161.1|CK035161
EST:     GGGGACCTACCAGTACGAGAACGCACACGTTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|33675031|gb|CF303270.1|CF303270
EST:     GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|29683509|gb|CB679784.1|CB679784
EST:     GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|88344996|gb|CI625842.1|CI625842
EST:     GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|58609841|gb|CK037874.1|CK037874
EST:     GGGGACCTACCAGTACGAGAACGCACAGGTTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|109974448|gb|DT806914.1|DT806914
EST:     CGAGAACGCACACATTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: CGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|84117031|gb|CD150798.1|CD150798
EST:     GTACGAGAACGCACACATTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
EST: gi|33677398|gb|CF305637.1|CF305637
EST:     GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAG                         GCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG
genomic: GGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCG

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: 72 (upstream exon), 56 (downstream exon)
Score: 36

TAATGAGGATGCACTCGTCTGGCATGAGGCAAACATACCATATGCAGTCTGGGGACCTACCAGTACGAGAACGCACACATTGACATACTATCCTTCTGAGgtatgatact ... ttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagacttgcattttattgacctataattttgaaaattggtatgtttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT
              tattgac  putative branch site (score: 36)
                                            tttctgcct  putative PPT
          attttattgacctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatactagctgttgtgatcttgtagacttgcattttattgacctataattttgaaaattggtatgtttctgcctagGCTATCAAGAACAATGGTTCTTTGTATGCTCATGTTTATTTTGCCCGCTCGGGTTACCCTGTGGATCCTACTGATCCTGAATATGAGCAAAGTTCTGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG