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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttttcattttaacatcgcaatatttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGATGTAA

Basic information

species Glycine max
transcript GLYMA20G23080.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 9
---gtaaacttttcattttaacat-cgcaatatttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGATGTAA
    | | || |    |||| | |  || ||  ||   ||   |  ||   |||  || ||   |||||     | |  ||    |||||||||||||| ||  |||| |||||| | ||  ||   ||||||||||| ||||| ||| | || ||||||||||| ||||| |||||||||| |    
gtaatcatctctatggtttaccctgtgctattcttaaattataa--ttcacatcctaa-tcaagcaagctacaaaatgcatgcaccagGTGAAATCTGGGACCATGTTCGACAATATTTTGGTTTGCGATGATCCTGATTATGCAAAGAAGCTTGCTGAAGAAACTTGGGGAAAGCACAAGGGT----

upper sequence: GLYMA20G23080.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 9
---------------------gtaaacttttcattttaacatcgcaatatttggtt-tgatacttttgga----tctgaactctgacaagcaggctattttatcttac-agGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGATGTAA
                      | |   ||| |||||   ||  |  |||||  || | |  |||   ||    |   || ||| | | |   |    |  || |  | |||||||||| || || ||||| ||||||||||| |||  ||||||||| || ||||| |||||| |||  ||||||||||||| |||| ||||||||    
gtaatgtctgttttgttttattttattcttttattttt-tatttctctatttaattctaaggcttcctgagcaattcaaattctaatatgtgaggatgtacatttggccagGTGAAATCAGGGACCTTGTTCGACAATGTCTTGATTTGTGATGATCCGGAGTATGCAAAGCAATTGGTAGAAGAAACATGGGCCAAGTACAAGGAT----
















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|13790097|gb|BG652688.1|BG652688
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATT
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATT
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     CTATATGTNTTTCCC-AACTTGAAGTACGTGGGCATTGAATTGGTGG-AG                         GTGAAATCTGGTACTTTGGTTGACAATGGCTTAATTAC
genomic: CTATATGT-TTTCCCCAACTTGAAGTACGTGGGCATTGAATTG-TGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTAC
EST: gi|5606713|gb|AI900811.1|AI900811
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGGTTGACAATGTCTTAATT
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATT
EST: gi|193341174|gb|FK306414.1|FK306414
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|193622041|gb|FK570453.1|FK570453
EST:     CAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGCACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: CAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|208317285|gb|GE117494.1|GE117494
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|208091443|gb|GD886338.1|GD886338
EST:     ACCTATATGTTTTCCCCAACTTGAAGTATGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGGAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGATGTAA
                         ctctgac  putative branch site (score: 3)
                                          ttttatctt  putative PPT
                                        tattttatcttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttttcattttaacatcgcaatatttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGATGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG