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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttgtttgtgttctttctacagtatactgttctgacttaattagctaagacttattaattttgtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG

Basic information

species Glycine max
transcript GLYMA10G41920.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 17
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 17
-----gtatatttgtttgtgt--tctttctacagtatactgttctgacttaattagctaagacttattaattttgtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG
     || | ||   |  ||   | ||  |   | | ||  ||||| || | ||   |  |||| ||  ||| | | |  | ||||||||||||| || || ||||    |||| |||  ||  ||||||||||||||||||||||||||||||  |||||||| ||||||||  |||||
gttctgtgtcttgtctgatgccattttctttgggaacacaattctgtctgagtt---tctgactgatccattctctatattcagGTTGTTATTACCAACCTAGAAGATGGCTCAATAACAGATCTTGATGCAAAGAAATGGCCTGATGCTCAAGAGGATGATGCATCTGCTTTTCACAAG

upper sequence: GLYMA10G41920.2 (Glycine max), 3'ss of exon 17
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 17
gtatatttgtttgtgttctttctacagtatactgttctgacttaattagc-taagacttattaattttgtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG
||  || | |     ||     |   ||  |||  ||  | || |||||      ||  |||  || | |  |   ||||||||||||| || |||||||     |||   || ||  |||||||||||||||||||||||||||||   || ||| | ||| | || ||||||
gtgcatctctc---atttgaagttgtgttcactaatc--attttattagtgctcaacggattctttctctggttccagGTTGTTATTACCAACCTTGAAGTTGGTTCAACGATGGATCTTGATGCAAAGAAATGGCCTGATGCTCAAATAGAAGATTCGTCTTCCTTTTACAAG
















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|17401220|gb|BM178002.1|BM178002
EST:     AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
genomic: AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
EST: gi|20812918|gb|BQ297396.1|BQ297396
EST:     CTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTCATTACTAATCTTGAAGCCAACTCAGCAATTGAGGTTGATGCAAAG
genomic: CTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
EST: gi|193469471|gb|FK436335.1|FK436335
EST:     AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
genomic: AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
EST: gi|19346023|gb|BM890903.1|BM890903
EST:     AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
genomic: AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
EST: gi|16995857|gb|BM085229.1|BM085229
EST:     AATTGAACAAAACAGCACCTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTCATTACTAATCTTGAAGCCAACTCAGCAATTGAGGTTGATGCAAAG
genomic: AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
EST: gi|298164021|gb|HO013666.1|HO013666
EST:     AATTGAACAAAACAGCACCTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTCATTACTAATCTTGAAGCCAACTCAGCAATTGAGGTTGATGCAAAG
genomic: AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
EST: gi|17401215|gb|BM177997.1|BM177997
EST:     AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAG                         GTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG
genomic: AATTGAACAAAACAGCTTCTCGTGCAATGGTTGTCCTACATCCACTCAAGgtatatttgt ... gtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacagtatactgttctgacttaattagctaagacttattaattttgtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG
                                   tattaat  putative branch site (score: 2)
                                         ttttgtctt  CT-rich tract
                            taagacttattaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttgtttgtgttctttctacagtatactgttctgacttaattagctaagacttattaattttgtcttgtaagGTTGTTATTACTAATCTTGAAGCCAACTCAGTAATTGAGGTTGATGCAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT