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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcactaggccatataacctatgcctcaagtccttttgcatcatgagcaagctttatgccaccaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA

Basic information

species Oryza sativa
transcript LOC_Os04g48820.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G114131_T02 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------aatcactaggccatataacc----tatgcctcaagtccttttgcatcatgagcaagctttatgcc-------accaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA
                                                                                        ||  ||    ||| ||       | ||  || |||  ||| | |||   |   | | || ||         | | ||| | | || |  | |   ||| | | |   ||||||||||| |||||||  || || ||||| |||||||| ||| | |  ||||||||||||||||||||||| || |||||||||||||||||  || | |
gttagtacttagcaatagcatgaaccctgtacttcatgttgcatgcttgtgtatcggttttgttagaaatttcagttgcatggtgaatattgctgtttcatctattaatggtctggttctagttgttt-gtatctaaatgtacccttttgattttttatatccataggtccat-aacaacagcaaactcttatcacagGTTGAAGTGTTCCAGCGACAGCTCGAACTAGCTAAGGAATTGGAGAGACCTGTTTCTGTTCATTGTGTGCGGGCATTTGGTGATCTTCTGGAAGTATTGA

upper sequence: LOC_Os04g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G26700.4 (Glycine max), 3'ss of exon 3
---aatcactaggccatataacctatgcctcaagtccttttgcatcatgagcaagctttatgccaccaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA
    ||        |||||| |     |   |  |     |   | |||   |||  |  | ||   | |        |  |  |   |  | ||   ||||| ||||||| ||   |||||| ||||||||||| || ||||| ||||| || |  |||||||||||||| || || |||||||||||||| ||| || | |
acacattgaccaatcatatatcaaggacagaagatgaccat---ttatgcagaagaatgctacctagattgttggctgctaatacattaggacatttgtgcagATTGAAGTATTGAGGCAGCAGCTTGAACTTGCAAAAGAGTTAAACAAACCAGCATCTGTTCATTGTGTTCGTGCTTTTGGTGATCTTCTTGAGCTAATGA

upper sequence: LOC_Os04g48820.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0024g00050.t01 (Vitis vinifera), 3'ss of exon 5
--------aatcactaggccat-ataacctatgcctcaagtccttttgcatcatgagcaagctttatgccaccaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA
            ||| |    | ||||   |   || |||   | ||    | |||  | | ||| ||     || |    |||  |    |  ||  |     | |||||||||||||||||||| || ||||||||||| || |||||||| |  || |||||||| ||||| || || || ||||||||||||||  ||||| |  
tcctactctcctacttgcttctgataatagaatgctaaagagatgtttt-ccttgaagatgttttgtga----aacagttttatttg----tttaattttctgttccagGTTGAAGTTTTCCAGCAACAGCTTGAACTTGCCAAAGAGTTGAAAAGACCAGTTTCTGTCCATTGCGTTCGTGCTTTTGGTGATCTTCTTCAGATAATGC

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|33795919|gb|CF323827.1|CF323827
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
EST: gi|218500580|gb|FG960548.1|FG960548
EST:     TTGGTCTGGACAC-G-TTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
EST: gi|33794900|gb|CF323330.1|CF323330
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
EST: gi|58689823|gb|CK078510.1|CK078510
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
EST: gi|66921923|gb|CX108771.1|CX108771
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTT-CCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCT
EST: gi|88413444|gb|CI581459.1|CI581459
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTTTCCAG
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAG
EST: gi|58690259|gb|CK078946.1|CK078946
EST:     TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAG                         GTTGAAGTTTTCCAGCAGCAACTTGAACTT
genomic: TTGGTCTGGACAAAGGTTCACATGGAAAAACCATTGACTTTGGAGAACAGgtttgtaatt ... atcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcaagctttatgccaccaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA
                                  agctaaa  putative branch site (score: 3)
                                 aagctaaaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcactaggccatataacctatgcctcaagtccttttgcatcatgagcaagctttatgccaccaataagactatcagaagctaaaaaatatcactgcagGTTGAAGTTTTCCAGCAGCAACTTGAACTTGCTAAGGAGTTGAACAAGCCTGTTTCTGTTCATTGTGTGCGCGCCTTTGGTGATCTTCTGGAGATACTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT