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

gttccattgtcttgaaatatgtaaaatatcagtttgttcatcttattgtttatgctaatgcattggtaattcatattcattgctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG

Basic information

species Oryza sativa
transcript LOC_Os03g11960.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11960.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G891739_T01 (Zea mays), 3'ss of exon 4
gttccattgtcttgaaatatgtaaaatatcagtttgttcatcttattgtttatgctaatgcattggtaattcatattcattgctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG
||||  |  |||||||  ||||| | ||| |   | || || ||             ||  | || |||   || |    |||||| ||||||||||| | || ||||||||||||||  ||||||||||||||||||| ||||||||| ||||||||||||| ||||
gttcggtcatcttgaaggatgtata-tataatcctattaattttg------------atcaactgataacctatttctgctgctttctgaagATTTCATTGAGTGGGCCTCATTCCATTCTGGGAAGGGCAGTTGTTGTACATGCTGATCCTGATGACCTAGGGAGGG

upper sequence: LOC_Os03g11960.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0007g07280.t01 (Vitis vinifera), 3'ss of exon 4
-----------gttccattgtcttgaaata-tgtaaaatatcagtttgttcatcttattgtttat-gctaatgcattggtaattcatattcattgctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG
            |||  | || |||  ||| ||| ||| |    ||  || ||  ||   || |  | | || | ||   || || |         |||||  |||||||| |||| ||||  ||||||||  ||||||||||||||||||| ||||||||| ||||||| || ||||| |
catttataaggtttctctagttttgtgataatgtgaaa-actttttgattgattatagacttaaaagtttattcctt--caactctttccttcaaatttgt--agATTTCATTAAGTGGGCAGCATTCCATTCTGGGAAGGGCAGTTGTTGTGCATGCTGATCCTGATGATCTTGGAAGAG
















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|88503033|gb|CI430539.1|CI430539
EST:     TGTTGCAGATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: TGTTGCAGATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|88518098|gb|CI445752.1|CI445752
EST:     GGTGTTGCAGATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: GGTGTTGCAGATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|88480951|gb|CI418222.1|CI418222
EST:     GGTGTTGCAGATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATT-GGAAGGGCAGTTGTTGTTCAT
genomic: GGTGTTGCAGATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|86527707|gb|CI167913.1|CI167913
EST:     GATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: GATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|88506655|gb|CI434161.1|CI434161
EST:     GGTGTTGCAGATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: GGTGTTGCAGATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|86533503|gb|CI173709.1|CI173709
EST:     TCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: TCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|88515699|gb|CI443353.1|CI443353
EST:     CAGATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: CAGATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
EST: gi|88489650|gb|CI426922.1|CI426922
EST:     GGTGTTGCAGATATCTTCATAAAGGACCTACAG                         ATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT
genomic: GGTGTTGCAGATATCTTCATAAAGGACCTACAGgttccattgt ... ctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcttattgtttatgctaatgcattggtaattcatattcattgctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG
               tgctaat  putative branch site (score: 2)
                                          ttgcttt  putative PPT
                             taattcatattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttccattgtcttgaaatatgtaaaatatcagtttgttcatcttattgtttatgctaatgcattggtaattcatattcattgctttgtgaagATTTCACTAAGCGGGCCTCATTCCATATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT