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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acctttcctataaccttgtgcactaggccgtacctttttgttttatttttcctgttaattaatgtggcttaattattctagaatctctatgtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTTTACAAGCAGCTTGTTAGCTCCGGACATGCATTTGGTGCAAAACGTTTGG

Basic information

species Glycine max
transcript GLYMA06G46000.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G46000.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0059g02310.t01 (Vitis vinifera), 3'ss of exon 7
----------------acct---ttcctataaccttgtgcactaggccgtacct--ttttgttttatttttcctgttaattaatgtggcttaattattctagaatctctatgtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTTTACAAGCAGCTTGTTAGCTCCGGACATGCATTTGGTGCAAAACGTTTGG
                | ||   | ||  |||     | | |||| | ||||    |||      |||  | ||  | | |  | |   |||||| ||||     |  | | |    |||||| ||||||||||||||||| ||||| |||||| |||||||||| ||| | || |||||| | |||| ||| || | ||||||||| || ||| | | ||
gtaaataaatgatcataactaaatgccactaaaaaactactctagccagtactgaatttcaacacattaatactaattagttctctcatttaatt-ttctgatggccttttatgcc-ttagGTTACATGGGTTGAGCATGTTGAAGTTGATGATCGAGGTGTTCATAATATATATAAGCAGTTAGTTAACTCTGGTCTTGCATTTGGGGCGAAAAGATGGG
















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|193410541|gb|FK379846.1|FK379846
EST:     GAAGGCCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAG                         GTCACATGGGTTGAGCA
genomic: GAAGGCCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAGgtacgagaca ... gtattattagGTCACATGGGTTGAGCA
EST: gi|193727711|gb|FK664509.1|FK664509
EST:     GAAGGCCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAG                         GTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTT
genomic: GAAGGCCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAGgtacgagaca ... gtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTT
EST: gi|193624296|gb|FK573392.1|FK573392
EST:     CCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAG                         GTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTT
genomic: CCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAGgtacgagaca ... gtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTT
EST: gi|193484236|gb|FK448562.1|FK448562
EST:     GAAGGCCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAG                         GTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTT
genomic: GAAGGCCTTCTGGCTGCCTAATTCAAGAAATGCCAAATGGCTATTCAAAGgtacgagaca ... gtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcctgttaattaatgtggcttaattattctagaatctctatgtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTTTACAAGCAGCTTGTTAGCTCCGGACATGCATTTGGTGCAAAACGTTTGG
                       ttaattattctagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acctttcctataaccttgtgcactaggccgtacctttttgttttatttttcctgttaattaatgtggcttaattattctagaatctctatgtattattagGTCACATGGGTTGAGCATGTGGAAGTGGATGATAGAGGTGTTCACAATCTTTACAAGCAGCTTGTTAGCTCCGGACATGCATTTGGTGCAAAACGTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
-cctttcc
- - - - - - - - - tgcacta
- - - - - - - - - - - - - -ccgtacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggctt