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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattcttaacagcaactgagcacaaaaagtcataaccattgttgtgcattagtttgacaggtttttcattttttttctacttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT

Basic information

species Glycine max
transcript GLYMA15G00570.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G00570.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G80840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaag-attcttaacagcaactgagcacaaaaagtcataaccattgttgtgcattagtttgacaggttt-ttcattttttttctacttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
||||| |||| | | |   |   | |     |  |    | | ||      | ||| |||    |||||  | ||| |     |  ||  ||  || ||||||||||||| ||||||||||||||||||||||| || ||||| ||||| || || ||||||||||| || ||||| ||  ||| |||||||||||
gtaagcattcatgaaaatgatcaaacttggtatctatctatctttagaa-actttattttatatggtttactgattgtagaagttgtttcttatagGTTGTGAAAGATGGGTATCAATGGAGGAAATATGGACAGAAAGTGACTAGAGACAATCCATCTCCAAGAGCTTACTTCAAATGTGCTTGTGCTCCAAGCT

upper sequence: GLYMA15G00570.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 3
gtaagattcttaacagcaactgagcacaaaaagtcata-accattgt-tgtgcattagtttgacag------gtttttcattttttttctacttgtttc-cagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
|||||      | |  ||| | |      |   |  |  |  ||| | ||  ||  |    || ||       |   ||      |||||   |||||  ||| | ||||| |||||||| || |||||||||||||| |||||||| |||||||| ||||| ||||| ||||| || ||||| |||||||||||||| ||||
gtaagtccaaaacccacaaataattggcgactttggtggattattctgtgaacaccatccggatagtgaatgatcgatcgagcaatttctttatgttttacagGTGGTGAAGGATGGATACCAGTGGAGGAAATATGGCCAAAAGGTCACCAGAGACAACCCCTCTCCGAGAGCCTACTTCAAATGCTCTTTTGCTCCTAGCT
















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|120491123|gb|EH219290.1|EH219290
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|17153505|gb|BM143438.1|BM143438
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|17401736|gb|BM178518.1|BM178518
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|13480260|gb|BG509603.1|BG509603
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|17518673|gb|BM187723.1|BM187723
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|209698492|gb|BW652384.1|BW652384
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|209717341|gb|BW659044.1|BW659044
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
EST: gi|15286185|gb|BI470076.1|BI470076
EST:     CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTT                         ATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA
genomic: CAAAAATTTCAAGAGTTTATATGAGGACAGAAGCATCTGATACAAGCCTTgtaagattct ... ttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccattgttgtgcattagtttgacaggtttttcattttttttctacttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT
                gtttgac  putative branch site (score: 4)
                          tttttcattttttttc  putative PPT
                          tttttcattttttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattcttaacagcaactgagcacaaaaagtcataaccattgttgtgcattagtttgacaggtttttcattttttttctacttgtttccagATTGTGAAAGATGGATATCAATGGAGGAAATATGGACAAAAGGTGACCAGAGATAACCCTTCTCCAAGAGCATATTTCAAGTGCTCTTTTGCTCCAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT