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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataattaattatataaacttttatcatttgagcggagattttgatggacaaattacacacagaaaatatgattttttgttaattatggaaaatctttaatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATCTCTTGGCTTTTTCCAT

Basic information

species Glycine max
transcript GLYMA12G06920.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06920.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g04460.t01 (Vitis vinifera), 3'ss of exon 5
gtaataattaattatataaacttttatcatttgagcggagattttgatggacaaattaca-cacagaaaatatgattttttgttaattatggaaaatctttaatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATCTCTTGGCTTTTTCCAT
    | | ||| ||| | | || |  | || |       ||| |||| ||    |||  |   ||||  | ||  ||| | | ||| |||   ||   ||| | |  ||||||||| | || ||||| ||| ||||||| |||||||||||||| || ||||| ||||||||| ||||||||||| |||| || ||||||||| |||| |
---gtgaataaatatctcatctctc-ttatgt-------gatgttgacggttggattctaatgcagattaaattgtttat-gctaactatctcaacctttttactcaaagGGACTGTTGACAGAAGGGTTTTTTTGGATTCCCTCTTTGGGTGGGCCAACTACAATTGCTGCTCGACAAAGTGGATCTGGCATTTCTTGGCTTATTCCGT
















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|120533265|gb|EH261398.1|EH261398
EST:     TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG                         GGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
genomic: TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataatta ... taatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
EST: gi|120533673|gb|EH261806.1|EH261806
EST:     TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG                         GGACTGCTAACCGAATGTTTTCTTTGGATCCCCTCTTT
genomic: TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataatta ... taatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTT
EST: gi|5760152|gb|AI965515.1|AI965515
EST:     CTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG                         GGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
genomic: CTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataatta ... taatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
EST: gi|120533657|gb|EH261790.1|EH261790
EST:     TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG                         GGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
genomic: TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataatta ... taatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
EST: gi|16105497|gb|BI893237.1|BI893237
EST:     TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG                         GGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGG
genomic: TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataatta ... taatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGG
EST: gi|10233625|gb|BE802513.1|BE802513
EST:     TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAG                         GGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT
genomic: TTCCAGTCTGGATTGGTCTCTACCAAGCTTTATCAAATGTGGCAAATGAGgtaataatta ... taatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacacacagaaaatatgattttttgttaattatggaaaatctttaatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATCTCTTGGCTTTTTCCAT
                                         tcttt  CT-rich tract
           aaaatatgattttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataattaattatataaacttttatcatttgagcggagattttgatggacaaattacacacagaaaatatgattttttgttaattatggaaaatctttaatttgaagGGACTGCTAACCGAAGGTTTTCTTTGGATCCCCTCTTTGGGTGGTCCTACTACCATTGCTGCTAGACAAAGTGGAGCTGGAATCTCTTGGCTTTTTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA