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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagcttcagagttatacagattctcatggtttgaaattattaccctgtgatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA

Basic information

species Glycine max
transcript GLYMA03G40000.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
lower sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 18
gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagcttcagagttat-acagattctcatggtttgaaattattaccctgtgatctatc---agGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
                            | ||  |  | |  ||  | |   | ||   | || |     || || ||| | |||  |||||   || |  |||  |   |||||||||| ||||| || || || ||||| |||||||| || |||||||| |||||  |||| || || ||  ||||||||||||| || ||||||||| 
---------------------------gtgcttgagccatacatggatctctgtttgttatttcttgtttatgcttatgttctgatgttatttgtctttattcttgcttaagGTTTCTGTTTTTGACTCGGTCGTGCAAGGCGGTGACTCTGTATGGGAAGGTCTTCGTATATACAAAGGGAAAGTATTTAAGCTTGAAGAACATCTAGACC

upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
lower sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagctt-cagagttatacagattctcatggtttgaaattattaccctgtgatct-atcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
          || ||   ||| ||||      | |  |||  | |   ||  | ||   || ||  |          || ||      |||| |    |  | |  | |||||||||| ||||| || ||||| ||||| |||||||| || ||||||||||||||  | || || ||||||||||| ||||||||||| ||||||||  
----------gtgtg---cttgaaatgtggaagaaaactt-aacagctcactgtttgttgatttgcattttgaacactgattatgttctatttcttcttatttttgtaagGTTTCTGTTTTTGACTCGGTTGTTCAAGGCGGTGACTCTGTATGGGAAGGACTTCGGATTTACAAGGGAAAGATATTCAAGCTTGAGGAACATCTAGATC

upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 18
gtaattaattgtatgacactt--aaaattcttctgtatg-ctttgatataacaaagcttcagagttatacagattctcatggtttgaaattattaccctgtgatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
||| |    | |  || | ||  | |||  | ||| |    ||| | || |   ||||      ||||   | |||| |||       || |||      |  | | | ||||||| |||||||| |||||||||||||| ||||| ||||| ||||| || |||||| | || || || ||||||||||||||||| |||||| |||| |
gtactcttatattggatatttggagaatcttcctggaaaattttaacatcattgagctctcagtttat---gtttctgatg------cataattttgtgattttttttaagGTTTCGGTGTTTGACTCTGTTGTCCAAGGTGGTGATTCAGTGTGGGAGGGGCTTCGAATTTACAACGGGAAGATATTTAAGCTTGAAGAGCATTTAGATA

upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S180_110V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------gtaat-taattgtatgacacttaaaatt---cttctgtatgctttgatataacaaagcttcagagttatacagattctcatggtttgaaattattaccctgtgatct-atcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
                                                   ||||  |   | | | | | | |    |     | | || ||  |    | | ||   || |  |       | || |  | ||    |      | | | |  |   ||||||||||||| ||||||||  |||| |||||||| ||   ||| ||||||||||||||  | ||||| || ||  | || ||||| ||||||||||||||||
gttagtgatgacaattctattgctccctttcgaaataactcaggaactttagtaaggtctctattttatattcaggtgtaagtatgtttaagcacttggttgagaagttttgaatgacgagttgtttttagtagtgcttatcagacatcattttcttggatcagGTTTCTGTATTTGATTCGATTGTGCAAGGAGGAGATGGAGTGTGGGAAGGACTTCGGATTTATAAGGGTAAAGTGTTCAAGCTAGAGGAGCATCTAGACA

upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 8
lower sequence: EFJ34717 (Selaginella moellendorffii), 3'ss of exon 8
gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagcttcagagttatacagattctcatggtttgaaattattaccctgtgatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
                                               ||||| ||      | |    ||   || |   || | ||| |   |||       ||||||||||||||||||||||| | || ||||| || |||   || |||||||| || ||  | || || || ||| | || ||||| | ||||||| ||||||
---------------------------------------------gtacaaacctcttttctaacctggagcttcttttgtttagattctcgtcct-------atcagGTTTCTGTGTTTGATTCTATCGTGCAAGGTGGAGACGGTGTCTGGGAAGGGCTCCGCATTTACAAAGGGAAGGTTTTCAAGCTGGGGGAGCATTTAGACA

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|151393608|gb|EV263483.1|EV263483
EST:     AATTGCTTGCTTGGGTTGGTGATGAGATTGTGACACGTGATAATGCAAAG                         GTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGAC
genomic: AATTGCTTGCTTGGGTTGGTGATGAGATTGTGACACGTGATAGTGCAAAGgtaattaatt ... gatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGAC
EST: gi|24205448|gb|BU964701.1|BU964701
EST:     AATTGCTTGCTTGGGTTGGTGATGAGATTGTGACACGTGATAGTGCAAAG                         GTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGA
genomic: AATTGCTTGCTTGGGTTGGTGATGAGATTGTGACACGTGATAGTGCAAAGgtaattaatt ... gatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGA
EST: gi|17021927|gb|BM092961.1|BM092961
EST:     AATTGCTTGCTTGGGTTGGTGATGAGATTGTGACACGTGATAGTGCAAAG                         GTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGA
genomic: AATTGCTTGCTTGGGTTGGTGATGAGATTGTGACACGTGATAGTGCAAAGgtaattaatt ... gatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagagttatacagattctcatggtttgaaattattaccctgtgatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA
                          tttgaaattatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaattgtatgacacttaaaattcttctgtatgctttgatataacaaagcttcagagttatacagattctcatggtttgaaattattaccctgtgatctatcagGTTTCTGTGTTTGATTCTGTTGTCCAAGGAGGTGACTCAGTTTGGGAAGGACTTCGAGTATATAATGGAAAGATATTTAAGCTTGAGGAGCATCTAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA