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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtcgttcggcccttgtgtcaggtagtgttgtagcataggtgctgaaaaattaattagttacaaataactacttaaagtaagctttttttgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGAGCAGGGGACCTTTTTGCAAGTGGATTTTTGTATGGAGTGGTCAAGGGTT

Basic information

species Glycine max
transcript GLYMA04G03290.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G03290.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g12750.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------ttgtcgttcggcccttgtgtcaggtagtgttgtagcataggtgctgaaaaattaattagttacaaataactacttaaagtaa----------gctttttttgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGAGCAGGGGACCTTTTTGCAAGTGGATTTTTGTATGGAGTGGTCAAGGGTT
                                     |      |           |    | || ||      | |    || | |||||  |   | |   |   || ||  |||||          | |   |||  ||  |||||| | | |||  | ||||| |||||  |||||||||| ||||| || |||||||||||||| |||||| ||||||||||||||||  | || |||||  
gttagtgcaatgtagctacactgcacttctgttgatatcacgaataaaatgcacattttacttgtatttagatgtggcctgtggagaattagctgcattctggttgttattttgagtaacatatggaatgttacctttttatttcagATGGTCCGAGTTGCAGCCATAGGGGAGGCAAAGGCAACTGATGCCACTGGAGCAGGGGACCTGTTTGCAGGTGGATTTTTGTATGGGTTAGTGAAGGGAC
















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|24205125|gb|BU964378.1|BU964378
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|193482421|gb|FK446176.1|FK446176
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|208330242|gb|GE129303.1|GE129303
EST:     TGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAAGGAG                         ATGATACAAGTCCCGG
genomic: TGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAA-GGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGG
EST: gi|192334034|gb|FK026191.1|FK026191
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|58020362|gb|CX707104.1|CX707104
EST:     CTGTTGTAACATTGGGTGTTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|208175425|gb|GD976820.1|GD976820
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|19053017|gb|BM731684.1|BM731684
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|10237995|gb|BE806883.1|BE806883
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|208323938|gb|GE120101.1|GE120101
EST:     CATTGGGTGCTAATGGGNGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|58016809|gb|CX703551.1|CX703551
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|209706385|gb|BW670788.1|BW670788
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|31462375|gb|CD404403.1|CD404403
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCTAACATGGAAAGGAG                         ATGATACTAGTCCCGGCCATTGGGGAAACTAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|208169509|gb|GD971880.1|GD971880
EST:     GTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATAACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGG
genomic: GTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGAT-ACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGG
EST: gi|10848246|gb|BF070781.1|BF070781
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|22930015|gb|BU547154.1|BU547154
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
EST: gi|12496252|gb|BG046971.1|BG046971
EST:     CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAG                         ATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA
genomic: CTGTTGTAACATTGGGTGCTAATGGGTGCATTGCCAAACATGGAAAGGAGgtgtgttaat ... tgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaaattaattagttacaaataactacttaaagtaagctttttttgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGAGCAGGGGACCTTTTTGCAAGTGGATTTTTGTATGGAGTGGTCAAGGGTT
                  aaataac  putative branch site (score: 2)
                                      ctttttttgc  putative PPT
     attaattagttacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtcgttcggcccttgtgtcaggtagtgttgtagcataggtgctgaaaaattaattagttacaaataactacttaaagtaagctttttttgcataccagATGATACAAGTCCCGGCCATTGGGGAAACAAAGGCAACCGATGCTACAGGAGCAGGGGACCTTTTTGCAAGTGGATTTTTGTATGGAGTGGTCAAGGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - -cccttgt
- - - - - - - - - - - ggtagtg
- - - - - - - - - - - - - - - - - - - - -tgctgaa