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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcactgtggtaattagacatatttctcagtttgaaatttaaaatatatgaggttcttgttttggcttatgtacagttttaatttatgtatgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os09g07830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 5
cttcactgtggtaattagacatatttctcagtttgaaatttaaaatatatgaggttcttgttttg---gcttatgtacagttt-taattt----atgtatgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG
       | ||  |||| ||  | |   ||||||     | ||| |||||   |||| |||||     || | |  || | || |||  |    |  ||   |||||| || || ||||||||||| |||||||| |||||||||| ||||||||| ||||| |||||||||||||||  ||||| |||||||||||  ||||| |||
-------gaggctatta-acgaagtggccagttttgttgtgaaagtatattctgttcatgtttaaagtgcatttcaactgcttataagcttgctaattacaattgcagGAAGGGGTCTCGTTTTGGTCATGACACACTTGTTGATGCCATGCTTAAGGATGGGCTTTGGGATGTATACAATGATTGTGCCATGGGAATGTGTGCCGAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 3
cttcactgtggtaattagacatatttctcagtttgaaatttaaaatatatgaggttcttgttttggct---tatgtacagttttaat------------ttatgtatgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG
               |  ||| | || ||||||| |  || ||| ||||||| ||||||||||    |   | |  || | ||||||             ||  ||    ||||| || || |||||||||||||||||||| |||||||||| ||||||||| ||||| |||||||||||||||  ||||| |||||||||||  |||||||||
---------------ttaacaaagttatcagttttattttgaaagtatatgatgttcttgtttaaagtggatttccactgctttaatacaataagcttgctaattacaaatgcagGAAGGGTTCTCGTTTTGGACATGACACACTTGTTGATGCCATGCTTAAGGATGGTCTTTGGGATGTATACAATGATTGTGCCATGGGAATGTGTGCTGAG

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 5
cttcactgtggtaattagacatatttctcagtttgaaatttaaaatatatgaggttcttgttttggcttatgtacagttttaa----tttatgtatgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG
     |    | ||| |   | |||||     ||        |||| |||||    ||  ||    ||  | ||   |   ||    | ||  || |  ||||| ||||| |||||||||||||||||||| |||||||||| ||||||||| ||||| |||||||||||||||  ||| | |||||||||||  ||||| || 
--atcccactgaaatcaaggaaatttcgggaatttccgaccgaaat-tatgaa-ccctgattccaactgctataatctggaaaatattctacatacgaatgcagGAAAGGGTCTCGTTTTGGACATGACACACTTGTTGATGCCATGCTTAAGGATGGACTTTGGGATGTATACAATGACTGTGCCATGGGAATGTGTGCCGAA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0089g00570.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------cttcactgtggtaattagacatatttctcagtttgaaatttaa------------aatatatgaggttcttgttttggcttat---gtacagttttaatttatgtatgtttgc---------------agAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG
                                        |  ||    || ||  ||||  |||||||| ||  |   ||            | || ||   |||   ||| |  || ||   |   ||| |  || ||| || | |  |               ||||| |||||||| || || ||||| ||| |||||||||| |||   ||||||||||| |||||||| |||   |||||||  |||| || |||||| || 
gttagctttttgggtcatgtgatcaattatgtctattgagttgcttgcttagtttaacatgattctcagtatgtgaacgaagcatgttgggccagtacatattgttgccgttcttactaatagggagaagtgtctatgtatctaagctgactctgagcttataaacagAAATGGATCTCGATTAGGCCATGATACTATTGTTGATGGTATGGCCAAAGATGGCCTCTGGGATGTTTACAACGATTTTGGAATGGCAATTTGTGCAGAA

upper sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 5
--cttcactgtggtaattagacatatttctcagtttgaaatttaaaatatatgaggttcttgt-tttggcttatgtacagttttaatttatgtatgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG
  |   ||  |  | |   ||  |||  ||||   | |  | | || |   | ||   |  |  |||  ||  ||   | || || | | |  |  || |||| || |||||||| |||||||||||  ||||||||||||| ||||| || ||||| || |||||||| ||| |||||   |  |||||   ||||||||| 
tacccaaccatactgacacga-gtataactcataatcagttctcaattgcttcagaagcaagaattttactggtgctta-ttctattgtctaaaaatt-gcagGAAGGGATCTCGATTTGGACATGATTCTCTTGTTGATGGAATGCTGAAGGATGGGCTGTGGGATGTTTACAGTGATACAGGGATGGGTGTTTGTGCTGAA

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|58685561|gb|CK074248.1|CK074248
EST:     GGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAG                         AAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGA
genomic: GGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAGgtctgcaaag ... atgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGA
EST: gi|29640957|gb|CB645964.1|CB645964
EST:     GGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAG                         AAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGA
genomic: GGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAGgtctgcaaag ... atgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGA
EST: gi|33678061|gb|CF306300.1|CF306300
EST:     GGTGGCATGGAAAGCATGTCTAATGCTCCAAAA-ACATTGCTGAAGCTAG                         AAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGA
genomic: GGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAGgtctgcaaag ... atgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGA
EST: gi|58683479|gb|CK072166.1|CK072166
EST:     GGTGGCATGGAAAGCATGTCTAATGCTCCAAA-TACATTGCTGN-GCTAG                         AAAAGGATCTCGTTTT
genomic: GGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGAAGCTAGgtctgcaaag ... atgtttgcagAAAAGGATCTCGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgaggttcttgttttggcttatgtacagttttaatttatgtatgtttgcagAAAAGGATCTCGTTTTGGACATGACACTCTTGTTGATGGCATGCTTAAAGATGGCCTTTGGGATGTATACGGTGATTTTGCCATGGGAAATTGTGCTGAG
                                ttttaat  putative branch site (score: 3)
                      ttatgtacagttttaa  TA-rich tract