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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgctgtaattgtagtggctttagtaatatttacatgactgagcaagttttaacatgataactgagcaagttttaacatatatttattttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCGGTTCCTGTTGGTGGTCTCG

Basic information

species Oryza sativa
transcript LOC_Os09g17840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g17840.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G307252_T02 (Zea mays), 3'ss of exon 4
gtgcgtgctgtaattgtagtggctttagtaatatttacatgactgagcaagttttaacatgataactgagcaagttttaacatatatttattttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCGGTTCCTGTTGGTGGTCTCG
||  |||||  ||||  ||||  || | ||  ||| |     ||   || |  ||  ||||   ||| |  | ||||                | | |||||||||||||||||  |||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| |
gtatgtgcttcaattccagtg-tttcattacaattgat----cttttcatgaatttgcatgg--actaaaaatgtttc---------------tatggcagCTTCTCTACAGGAAATACAGTGGAAATTTCCTTGTTAACCTTCTTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCTGTTCCGGTTGGTGGTCTTG
















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|58691276|gb|CK079963.1|CK079963
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|58609448|gb|CK037481.1|CK037481
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|27577144|gb|CA999838.1|CA999838
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|58677615|gb|CK066302.1|CK066302
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|11442629|gb|BF430532.1|BF430532
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|27578160|gb|CB000855.1|CB000855
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|218481280|gb|FG947521.1|FG947521
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|58596248|gb|CK006776.1|CK006776
EST:     CCATCATTCTGCACTCTGCACTGATTGCCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|27576829|gb|CA999523.1|CA999523
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|33679126|gb|CF307365.1|CF307365
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|58676853|gb|CK065540.1|CK065540
EST:     CATCATTCTGCACTCTGCAGCTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CATCATTCTGCACTCTGCA-CTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
EST: gi|58664069|gb|CK052755.1|CK052755
EST:     CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAG                         CTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA
genomic: CCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAA

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), 75 (downstream exon)
Score: 83

GGGGCAGCAAGGCTCATATCCAATTAAGTTGTTCTACACTTCAAACATGCCCATCATTCTGCACTCTGCACTGATTACCAACCTCTACTTCATATCACAGgtgcgtgctg ... tttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCGGTTCCTGTTGGTGGTCTCG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaagttttaacatgataactgagcaagttttaacatatatttattttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCGGTTCCTGTTGGTGGTCTCG
                            ttttaac  putative branch site (score: 83)
                                        tttatttt  putative PPT
                         aagttttaacatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgctgtaattgtagtggctttagtaatatttacatgactgagcaagttttaacatgataactgagcaagttttaacatatatttattttgttgcagCTTCTCTACAGGAGGTACAGTGGAAATTTTCTGGTTAACCTTCTTGGGAAATGGAAGGAATCTGAGTACTCTGGCCATTCGGTTCCTGTTGGTGGTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG