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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

Basic information

species Glycine max
transcript GLYMA10G31310.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os04g56480.1 (Oryza sativa), 3'ss of exon 6
------------------------------------------------------------------------------------------------------tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
                                                                                                      |   |  |  |  ||  | |   |  |  ||   ||     |   | | ||  | |  |  |||  | || | || |  ||  | ||  ||   ||| || || || || ||  |  | || || |||||||| |||||||| || ||||| ||||| |||||||||||||||   
gtaagttgagtcattgactcattgtgccatggcacgaccaagataatttttattgtacttcccatgatagcatgctaattgtgatgatgaaagagtattatcttaatagtagccctgtttgattccctattcttttaaaggcttgagttacctctt-gcggtgattgtatttgacttat--tagctatggttatctaaacagCATAACAGTAACCAGAGCACGTATTGAAACATCTATTCCTCGGAAGCATGGCCCTGCGATTGCTGGTTATGAGTCG

upper sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G044011_T01 (Zea mays), 3'ss of exon 7
tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaat----aaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
|||||     ||     |       || |||  || ||| ||   | |      |    |||||   ||  |  || | |  |  ||| | ||     ||| || || || |  || ||  | || || ||||||||||||||| | || ||||| |||||||||||||| || ||||  
tggttagcagctacatatttt----aagactttaatttatatttttaactgaagaacacatattgctatatagatggcatcctgatgtatcattttctaaacagCATAACAGCAACCCGGGCACGTATTGAAACATCAATTCCTAGGAAGCATGGCCCTGCAATTGCTGGCTACGAGACG

upper sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G27650.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------------------------------------tggttgatttctgtgggtaaccacaaacac-tggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
                                                                                |  || |  |  |||| |       ||||  |   ||     |  | ||  |||   |  |  | ||   |  |||   ||||   |||||  |     ||| ||||   ||  ||| | || ||||||||||| |||||| | || ||||| ||||||||||||||||| |||   
gtactgattgcagtgacaaggtccattgtctgtgaaatttgttatttcctagtttttgttttgacaacatgtagttctcttatttcacctgggtggttttggctgaacaagtatgaaacgggtcaaagaaattc--atccaattctgttcttgtttactttat---tgtcttgtttggcagTGTGACAAGTAGCCGTGCACGAATAGAAACATCCATTCCTAGGAAGCATGGACCTGCAATTGCTGGTTACGAGTCT

upper sequence: GLYMA10G31310.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g00140.t01 (Vitis vinifera), 3'ss of exon 7
tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtc-ttatttttgtctaa--taaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
          ||     | |   | ||   |  | |||   |     || || ||    || ||  | ||  |    | ||| |  ||   ||  |  || ||  | ||  ||||||| || ||||||||| | |||||||||||||||||||||||||| |||||||||||||||  |
aaagcatgcccttcacattagtgctaatttttcatattttttgtggcatattttac---atgttcaactttctcatccattactgctgctaaaatttcaacagCCTTACAATTACTCGCTCCCGGATAGAAGCTTCAATTCCTCGCAAACATGGGCCTGCTATTGCTGGTTATGAGGCA

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|193624268|gb|FK574260.1|FK574260
EST:     GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|207778021|gb|GD747954.1|GD747954
EST:     GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|193650755|gb|FK595878.1|FK595878
EST:     CCTCCTTGTTGGTAGAAG                         TATGACTGTTACCCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: CCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|9898819|gb|BE607787.1|BE607787
EST:     GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|208083199|gb|GD879229.1|GD879229
EST:     GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|193472093|gb|FK437096.1|FK437096
EST:     CCTCCTTGTTGGTAGAAG                         TATGACTGTTACCCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: CCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|208087721|gb|GD888581.1|GD888581
EST:     TGGTTGTAGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: TGG-TGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|23731912|gb|BU764103.1|BU764103
EST:     TTGATGCAAGAAGGTTTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: TTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
EST: gi|208119461|gb|GD917394.1|GD917394
EST:     GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAG                         TATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG
genomic: GTGGTGTTGATGCAAGAAGGATTAGCCCATATCCTCCTTGTTGGTAGAAGgttaactttc ... aataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA
                                         gtctaat  putative branch site (score: 3)
              atatttgaattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggttgatttctgtgggtaaccacaaacactggaaattaaatacatgatcttctagttgatatttgaattaatttgtcttatttttgtctaataaaatagTATGACTGTTACTCGTTCGCGGATAGAAACATCAATTCCTCGCAAACATGGGCCTGCAATTGCTGGTTATGAGAAA

- - - - -tctgtgg
- - - - - - - - - - - -caaacac
- - - - - - - - - - - - - - - - -aaattaaa
- - - - - - - - - - - - - - - - - - - - - -catgatc