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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaaaatgttgtagcacgatgtcagcaattttattttaagttgtttgttatggaatggttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG

Basic information

species Glycine max
transcript GLYMA16G01680.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01680.2 (Glycine max), 3'ss of exon 3
lower sequence: AT5G50430.2 (Arabidopsis thaliana), 3'ss of exon 3
aggaaaatgttgtagcacgat-gtcagcaattttattttaagt-tgtttgttatggaatggttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
| | | ||| | | | || | | || | | | | | |||| || || | | |||| ||| || ||| | ||| | | |||||||||||||||| || ||||| ||||| ||||||||||
tgctacaagttagggtatttttatcctcgctactagtgttactgcactatttatataaatgtagtcaattgagtttgaact-attgggttttattcta-cagATTATGTGTTGGAAGGCAGTGAGGGAACGCCTTTTGCAG

upper sequence: GLYMA16G01680.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G17280.1 (Arabidopsis thaliana), 3'ss of exon 3
aggaaaatgttgtagcacgatgtcagcaattttattttaagttgtttgttatggaatggttgatacttgat---actgaccttattctat---gttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
||| || | | | | | || ||| || | || | ||||| | | | | ||| |||| ||||| | ||||||||||| |||| || ||||| ||||||||||||||||
----gggagtttcagtct--ttctattattactgcatttagtatgttaaaaagggtagcttgatctcttactaaaatagagttaaactattggattaatcttacagATTATGTGCTGGAAGGCAGTGAGGGAACACCTTTTGCAG

upper sequence: GLYMA16G01680.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g00280.t01 (Vitis vinifera), 3'ss of exon 4
aggaaaatgttgtagcacgatgtcagcaattttattttaagttgtt--tgttatggaatggttgatac-ttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
| | ||||| | | | |||||||| | | || | || | || ||| || ||||| | || | ||| || |||| |||||||||||| ||||||||||||| |||||||| |||||||
ggtattatgtttttctctcactttcctgattttattatggtctattaattttcttgagcatttgtaaccttgatttta---ttctcctaccttgatgtttcagATTATGTGCTGGAGGGAAGTGAGGGAACACCGTTTGCAG

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|17964448|gb|BM271183.1|BM271183
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|16349197|gb|BI974792.1|BI974792
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|151399625|gb|EV269496.1|EV269496
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|192330701|gb|FK022314.1|FK022314
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|13790033|gb|BG652624.1|BG652624
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|298194643|gb|HO043115.1|HO043115
EST:     AGCTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
EST: gi|19936822|gb|BQ081027.1|BQ081027
EST:     AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGC                         ATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAGGTGGATAT
genomic: AGTTTCTCATGTTGTGGCTCGTCCTTCACCGAGTGATATTCTTGAGTGGCgtaagtttgt ... aatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAGGTGGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttatggaatggttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG
                                 ttattctatgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaaaatgttgtagcacgatgtcagcaattttattttaagttgtttgttatggaatggttgatacttgatactgaccttattctatgttaatgtctcagATTATGTGTTGGAGGGAAGTGAAGGAACACCTTTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA