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'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaggtttttcagtagtaatagttcttatctgtgaatcttgtgttctcatgttctgcttttgaattgttttattttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC

Basic information

species Glycine max
transcript GLYMA16G32960.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g04510.1 (Oryza sativa), 3'ss of exon 6
gtatgtgaggtttttcagtagtaatagttcttatctgtgaatct-tgtgttctcatgttctgcttttgaattgttttattttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC
|| ||| |       ||   | |   ||   || || ||    | ||     |||    ||  |  | ||   |       || ||||||||||| ||||| ||||||||||||||| | || || ||||| ||  | |||||||| ||||||||||| || ||||| ||||| || || || ||||
gtctgttaaa-----caactgcatcggtatataactttgttcttctgaaacttcagaaccta-tgctaaaacatcaagaaattgcagCACATTGCAAATCTTGCTGGAAACAAGACTCTCGTGCTGCCTGTACCCGCTTTCAATGTGATCAATGGAGGATCCCATGCTGGAAACAAACTTGCCATGC

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G446253_T01 (Zea mays), 3'ss of exon 5
gtatgtgaggtttttcagtagtaatagttcttatctgtgaatcttgtgttctcatgttct-------gcttttgaattgttttattttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC
         || |||||    | |  | | | || | | | | |  |||   ||   | |       |   |  || | |  |  |||||||||||||||| ||||| ||||||||||| ||| |||| || ||||| ||| | || ||||| || |||||||| |||||||| ||||| ||||| || ||||
---------gtctttcaagcattaccgctatgatttattattgtgttgtatgcacaatttagagagcgtactgaaagtttacttatttttcagCACATTGCAAATCTTGCTGGAAACAAAACTCTGGTGCTCCCTGTACCTGCCTTTAATGTGATTAATGGAGGATCACATGCTGGAAACAAGCTTGCCATGC

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G064302_T01 (Zea mays), 3'ss of exon 6
gtatgtgaggtttttcagtagtaatagttcttatctgtgaatcttgtgttctcatgttctgcttttgaattgttttatt-ttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC
|| | | |  | |  | |   | ||  || |  | |||   | |       | |     ||   |  ||  ||||  || ||| |||||||| || ||||| ||||||||||| ||| |||| || ||||| ||| | || || || || |||||||| |||||||| ||||| ||||| || ||||
gtctttcaaatgtcactgctatgatttttttattatgttggtatgcacaatttagagggtgtcctgaaa--gtttagttatttgcagCACATCGCAAATCTTGCTGGAAACAAAACTCTGGTGCTCCCTGTACCTGCCTTTAACGTGATTAATGGAGGGTCACATGCTGGAAACAAGCTTGCCATGC

upper sequence: GLYMA16G32960.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv16s0022g01770.t01 (Vitis vinifera), 3'ss of exon 6
-----gtatg---tgaggtttttcagtagtaatagttcttatctg------tgaatcttgtgttctcatgtt-ctgcttttgaattgttttatttttt-cagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC
     |||||   |    |  |||| |  || |  || | | ||       || ||    | |||| |  |   | || |||  |   ||| |    | ||||||||||||||||| ||||||||||| |  || || || ||||| ||| |||||||||||||||||||||| || ||||| || || || ||||| ||||
gtacagtatgcagtagcataattcattcatagttattttaaactaattacatgcataaatttttcttacatgattactcttgtttatatttgtaccctgcagCACATTGCTAATCTTGCTGGAAACAAAAAGTTAGTGCTGCCTGTACCTGCATTCAATGTTATCAATGGAGGTTCTCATGCTGGCAACAAACTAGCCATGC

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|254320422|gb|GR826871.1|GR826871
EST:     TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG                         CACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
genomic: TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgagg ... attttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
EST: gi|254317870|gb|GR832038.1|GR832038
EST:     TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG                         CACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
genomic: TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgagg ... attttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
EST: gi|24135559|gb|BU926069.1|BU926069
EST:     TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG                         CACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
genomic: TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgagg ... attttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
EST: gi|213611484|gb|DB959194.1|DB959194
EST:     TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG                         CACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
genomic: TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgagg ... attttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
EST: gi|213587887|gb|DB959711.1|DB959711
EST:     TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG                         CACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
genomic: TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgagg ... attttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
EST: gi|254343118|gb|GR859280.1|GR859280
EST:     TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAG                         CACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA
genomic: TTGCTGTCTGTAAGGCTGGTGCTGCAGTGAAGAAAATTCCTCTGTACAAGgtatgtgagg ... attttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgtgaatcttgtgttctcatgttctgcttttgaattgttttattttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC
                                      ttgttttattttttc  CT-rich tract
                               ttttgaattgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaggtttttcagtagtaatagttcttatctgtgaatcttgtgttctcatgttctgcttttgaattgttttattttttcagCACATTGCTAATCTGGCTGGAAACAAGACTTTGGTACTACCTGTGCCTTCATTCAATGTTATCAATGGAGGCTCACATGCAGGAAATAAGCTAGCAATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG