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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatctgatatttaagatatttgcatgttttctttacaagctcctggttgcgtgagcacaacctgttttggttggttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCTGAGTGTCGCCACCTTATCTCAAGGATCTTTGTTTTTGACCCTGCAGAG

Basic information

species Glycine max
transcript GLYMA01G39020.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39020.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0197g00080.t01 (Vitis vinifera), 3'ss of exon 7
gttgatctgatatttaagatatttgcatgttttctttacaagctcctggtt---gcgtgagcacaacctgttttggttggttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCTGAGTGTCGCCACCTTATCTCAAGGATCTTTGTTTTTGACCCTGCAGAG
          ||||| |         ||  || | | |  |     || |       | | |  ||  ||       |  || | |||||||  |||||||||| |||||||||||||||  |  ||||||| ||||| | ||||||| |||||| ||||||||||| ||||||  |||||||| || |
---------gtatttcactaggccttattattgcatcatgaatctgtgatatgaatctcatctgaaaatgccccttattatttcatgcagAGAATTCTCAGTGTTCAGTATTCCATTCCAAGCTCTGTTCAAATATCTACCGAGTGTCACCACCTGATCTCAAGGATATTTGTTGCTGACCCTGGAGCG
















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|58015703|gb|CX702445.1|CX702445
EST:     ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAG                         AGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT
genomic: ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAGgttgatctga ... ttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT
EST: gi|7693434|gb|AW761526.1|AW761526
EST:     ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAG                         AGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTTTCTCCT
genomic: ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAGgttgatctga ... ttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT
EST: gi|21888347|gb|BQ741560.1|BQ741560
EST:     ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAG                         AGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTTTCTCCT
genomic: ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAGgttgatctga ... ttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT
EST: gi|27424851|gb|CA936371.1|CA936371
EST:     ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACA-TTCAG                         AGGGGTCTCAGTGTCCAGTATTCCA
genomic: ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAGgttgatctga ... ttccttgcagAGGGTTCTCAGTGTCCAGTATTCCA
EST: gi|11413312|gb|BF425323.1|BF425323
EST:     ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAG                         AGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTTTCTCCT
genomic: ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAGgttgatctga ... ttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT
EST: gi|58015395|gb|CX702137.1|CX702137
EST:     ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAG                         AGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT
genomic: ATCCTTTTGAAGATCCTAATGATCCAAAGGATTTCCGGAAGACAATTCAGgttgatctga ... ttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttacaagctcctggttgcgtgagcacaacctgttttggttggttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCTGAGTGTCGCCACCTTATCTCAAGGATCTTTGTTTTTGACCCTGCAGAG
                                             ttccttgc  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatctgatatttaagatatttgcatgttttctttacaagctcctggttgcgtgagcacaacctgttttggttggttccttgcagAGGGTTCTCAGTGTCCAGTATTCCATTCCAGACAATGTTCAAGTATCTCCTGAGTGTCGCCACCTTATCTCAAGGATCTTTGTTTTTGACCCTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG