Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttagtaccctactaccctttatttttcatcattgttttttgtttacaatttctgtttttgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGATCACGAGCGTGTTGTTGATTGCACTACTCCCAATTTTAATGG

Basic information

species Glycine max
transcript GLYMA17G00250.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G00250.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv10s0071g01040.t01 (Vitis vinifera), 3'ss of exon 1
------------------------gtcttagtaccctactaccctttatttttcatcattgttttttgtt-tacaat--------ttctgtttttgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGATCACGAGCGTGTTGTTGATTGCACTACTCCCAATTTTAATGG
                         ||| || |   ||   |||||  ||||||||||   |||  | || |||||         || || ||||||| | ||||||||||||||||||||||| || ||| | |||||||||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||
gtctttcctttttctctgtttggtttctcag-agagtaaagcccttcctttttcatcaggctttgatattatacaaaaaaacgggttttgcttttgttccgcagTTCAGAGAGTCAGGCTGTGAAAATTGCCCCTTCTTTAAGATGGATGAAGACCATGAGCGTGTTGTCGATTGCACTACTCCTAATTTTAATGG
















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|4396313|gb|AI495310.1|AI495310
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATG---A-                         -TCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|151409763|gb|EV279571.1|EV279571
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|298194297|gb|HO040945.1|HO040945
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGGT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|254326666|gb|GR832818.1|GR832818
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|298184274|gb|HO029487.1|HO029487
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|298166707|gb|HO010146.1|HO010146
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|192300665|gb|FG991077.1|FG991077
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|192326423|gb|FK015925.1|FK015925
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|298178229|gb|HO023964.1|HO023964
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|7795909|gb|AW781306.1|AW781306
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
EST: gi|15286015|gb|BI469906.1|BI469906
EST:     ATGAGTTGAGGGCTTGTCTTCGTTGTCGCCTTGTCAAAACCTATGATCAG                         TTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT
genomic: ATGAGTTGAGGGCTTGTCTTCGTTGCCGCCTTGTCAAAACCTATGATCAGgtcttagtac ... tgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accctttatttttcatcattgttttttgtttacaatttctgtttttgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGATCACGAGCGTGTTGTTGATTGCACTACTCCCAATTTTAATGG
                                   tttctgtttttgtttc  CT-rich tract
     ttatttttcatcattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcttagtaccctactaccctttatttttcatcattgttttttgtttacaatttctgtttttgtttcacagTTCAGAGAGTCAGGCTGTGAGAACTGCTCATTCTTTAAGATGGAAGAAGATCACGAGCGTGTTGTTGATTGCACTACTCCCAATTTTAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA