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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

Basic information

species Glycine max
transcript GLYMA20G24070.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 10
------------gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatg--------attatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
             | |  |  |||   | |   | |  | |  |   |   |  || |||| | |||         ||| |  | |    | ||  ||||||||||| || |||||||||||||| || || || || || || || ||||||||||| |||||||||||| |||| ||||||
ttgcgttggatctttaccatttatgttattacctaatgtgtgctttgtttagtcttaaacaataaatatgtttaacattgtgctgtttcatcctaaacagATATTACACATCCAACTCCTGATCTTACGGGGTACATTACCGAAGGACAGATATACATTGACAGGCAGCTGCATAACAGACAG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G094497_T03 (Zea mays), 3'ss of exon 1
------------gtaatgaa--atatagaagttaatcagctatcttgcataat-ggttttaacactgaatgatta-tattttgaacttctgt----acagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
             | ||||   || ||  |  || |    | | |||   | |   |  ||  |    |||  || |||| | | || |       |||||||| || |||||||||||||| || || ||||| || |||||||| ||||||||||| || ||||||||  |||| ||||||
tagcatgttggtctcatgatttatttaccatctatttcattttgttgggcatttaatactagtataccatgtctaatattgtaatctacccctaaaacagATATCACACACCCAACTCCTGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
-----------------------gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgta-cagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
                        |   ||     | ||  |  |  || || |  |  ||   |   |   || |   ||| || | |  ||| ||  | ||||||| || ||||||||||| || || || ||||| || |||||||| ||||||||||| || ||||||||  |||| ||||||
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaagtataccatggctaat--attgtaatct--actcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 10
gtaatgaaatatagaagtta-atcagctatcttgcataatggttttaacactgaatgattatattt--tgaactt---ctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
||||||  |   |  |   | ||        | |    |   | | |  |  |    | || | |   ||||| |    |  |||||||| || || || ||||| ||||| || || |||||||||||||| ||||| ||||| ||||| |||||  | ||| |||||
gtaatgtcaagcatcatccatattgatctagtggtgagaatttctcattatagtggcactacactcactgaacctgattttcacagATATAACACATCCCACTCCCGATCTCACGGGTTATATCACTGAGGGCCAGATTTACATTGACAGACAGCTCCACAATCGACAG

upper sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 11
lower sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------------gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
                                                                                       |  |  | |        |  ||  || |    | |     | |    ||| |         || ||   ||  || |||||||||| ||||||| ||||||||| ||||||||||| || || || || || ||  | ||  ||||| |  | || ||||||
gtcagttgcatccttcctttgtcatcaagtttcagtatttgctttctttgaaatgggcattttactttgttatattatttttgctctttcttgactgcgtgcagtcttcgactgtgg-acttctccttgtctgtactaagcttcacctttgtggcatttcgtgcagATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG

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|16276790|gb|BI942045.1|BI942045
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|21256304|gb|BQ453192.1|BQ453192
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|193476671|gb|FK439532.1|FK439532
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16279439|gb|BI943437.1|BI943437
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACACGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|207826377|gb|GD800678.1|GD800678
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|208048001|gb|GD848752.1|GD848752
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTG
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTG
EST: gi|16276744|gb|BI942021.1|BI942021
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16279488|gb|BI943462.1|BI943462
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCCATGATG                         ATATTACGCANCCCAACTCC
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCA-CCCAACTCC
EST: gi|16278548|gb|BI942962.1|BI942962
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|19346883|gb|BM891771.1|BM891771
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGA
EST: gi|16279486|gb|BI943461.1|BI943461
EST:     GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATG                         ATATTACGCACCCAACTCCTGATCTAACACGATATATCACTTGAGGG-CAG
genomic: GCGTAAAGGCTCTATTACACAAATTCCAATTCTAACCATGCCCAATGATGgtaatgaaat ... ttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACT-GAGGGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcttgcataatggttttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG
                ttttaac  putative branch site (score: 2)
                                            cttctgt  putative PPT
                           aatgattatattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaaatatagaagttaatcagctatcttgcataatggttttaacactgaatgattatattttgaacttctgtacagATATTACGCACCCAACTCCTGATCTAACAGGATATATCACTGAGGGGCAGATATACATCGACAGGCAGCTGTATAATAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG