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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatgacagtagaaaactcctgtaccaaagttcgatgcttgtattatattttttttctgcaaattcatgtaaaaaacatcctgggggatacctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAAGATTTCAGTAAGACGAAATCTGGTAAGGAACACTTGGATGAAGGTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g49250.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49250.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G073045_T01 (Zea mays), 3'ss of exon 6
-----------------------ctcatgacagtag-aaaactcctgtacca----aagttcgatgcttgta-ttatatttt--ttttctgcaaattcatgtaaaaaacatcctgggggatacctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAAGATTTCAGTAAGACGAAATCTGGTAAGGAACACTTGGATGAAGGTGAAG
                        | |  |   ||  || | ||||  | ||    |||||  ||  || |  || ||   |  || |||| ||   ||||    |||| | | |  | ||  ||| ||||||| |||| || || || |||||||||||||||||| |||| || |||||||||||||  ||||  |||| ||| |||||  || |||||||||||| | 
gtcagtactttctcctataggcttttaaaattatattaagattccttcatcagttgaagttttatctttatgcttgtaccctcattatctgtaagggcatg----aaactttcggttgcatctctcctcagGTCATAACGTCATGTAATCACACAAAGGATGAGCTTCTGCATGAAGTAGAAGATTTCACCAAGAGAAAATTTGGCAAGGAGAACGTGGATGAAGGTGCAC
















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|29631535|gb|CB636544.1|CB636544
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|87006979|gb|CI275287.1|CI275287
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|88989955|gb|CI018832.1|CI018832
EST:     ATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: ATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86496381|gb|CI139014.1|CI139014
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86501869|gb|CI144502.1|CI144502
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86859443|gb|CI278855.1|CI278855
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|87007116|gb|CI277191.1|CI277191
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86501397|gb|CI144030.1|CI144030
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86414904|gb|CI069307.1|CI069307
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86499771|gb|CI142404.1|CI142404
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86503540|gb|CI146173.1|CI146173
EST:     GAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: GAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86499492|gb|CI142125.1|CI142125
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86501021|gb|CI143654.1|CI143654
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|88223681|gb|CI223530.1|CI223530
EST:     GTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: GTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|86828266|gb|CI276855.1|CI276855
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|88228528|gb|CI228008.1|CI228008
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA
EST: gi|88996040|gb|CI037331.1|CI037331
EST:     TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTG                         GTCGTAACATCGTGCAACCACACNAAGGATGAGCTTGTGCAAGAGGTAGAA
genomic: TAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAA

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: 52 (upstream exon), 65 (downstream exon)
Score: 12

AGTAATGTATTGGGAGTCTGTATCGAACTTGGTTGAACCTGGTGGCATTGTGgtcagtactt ... acctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAAGATTTCAGTAAGACGAAATCTGGTAAGGAACACTTGGATGAAGGTGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattttttttctgcaaattcatgtaaaaaacatcctgggggatacctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAAGATTTCAGTAAGACGAAATCTGGTAAGGAACACTTGGATGAAGGTGAAG
                                            tacctcttc  CT-rich tract
                aaattcatgtaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcatgacagtagaaaactcctgtaccaaagttcgatgcttgtattatattttttttctgcaaattcatgtaaaaaacatcctgggggatacctcttcagGTCGTAACATCGTGCAACCACACAAAGGATGAGCTTGTGCAAGAGGTAGAAGATTTCAGTAAGACGAAATCTGGTAAGGAACACTTGGATGAAGGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- catgaca
- - - - -gtagaaaa
- - - - - - - - - -cctgtac
- - - - - - - - - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catcctg