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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacttttcattttaacatcgcaatatttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGAT

Basic information

species Glycine max
transcript GLYMA20G23080.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0005g01390.t01 (Vitis vinifera), 3'ss of exon 9
---gtaaacttttcattttaacat-cgcaatatttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGAT
    | | || |    |||| | |  || ||  ||   ||   |  ||   |||  || ||   |||||     | |  ||    |||||||||||||| ||  |||| |||||| | ||  ||   ||||||||||| ||||| ||| | || ||||||||||| ||||| |||||||||| |
gtaatcatctctatggtttaccctgtgctattcttaaattataa--ttcacatcctaa-tcaagcaagctacaaaatgcatgcaccagGTGAAATCTGGGACCATGTTCGACAATATTTTGGTTTGCGATGATCCTGATTATGCAAAGAAGCTTGCTGAAGAAACTTGGGGAAAGCACAAGGGT

upper sequence: GLYMA20G23080.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 3'ss of exon 9
---------------------gtaaacttttcattttaacatcgcaatatttggtt-tgatacttttgga----tctgaactctgacaagcaggctattttatcttac-agGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGAT
                      | |   ||| |||||   ||  |  |||||  || | |  |||   ||    |   || ||| | | |   |    |  || |  | |||||||||| || || ||||| ||||||||||| |||  ||||||||| || ||||| |||||| |||  ||||||||||||| |||| ||||||||
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|193341174|gb|FK306414.1|FK306414
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|254340600|gb|GR850902.1|GR850902
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|31469544|gb|CD411572.1|CD411572
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|13790097|gb|BG652688.1|BG652688
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATT
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATT
EST: gi|31311102|gb|CD396305.1|CD396305
EST:     GGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: GGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|7147510|gb|AW509432.1|AW509432
EST:     CTATATGTNTTTCCC-AACTTGAAGTACGTGGGCATTGAATTGGTGG-AG                         GTGAAATCTGGTACTTTGGTTGACAATGGCTTAATTAC
genomic: CTATATGT-TTTCCCCAACTTGAAGTACGTGGGCATTGAATTG-TGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTAC
EST: gi|6094883|gb|AW119550.1|AW119550
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|58021776|gb|CX708517.1|CX708517
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|213596806|gb|DB978038.1|DB978038
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|192307920|gb|FK003068.1|FK003068
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|26268307|gb|CA819370.1|CA819370
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|254340601|gb|GR850903.1|GR850903
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|209711758|gb|BW678940.1|BW678940
EST:     CCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: CCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|5606713|gb|AI900811.1|AI900811
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGGTTGACAATGTCTTAATT
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATT
EST: gi|208042272|gb|GD839550.1|GD839550
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|208301469|gb|GE099861.1|GE099861
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|16997164|gb|BM086536.1|BM086536
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|6915349|gb|AW396879.1|AW396879
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|5126765|gb|AI748501.1|AI748501
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|193382511|gb|FK345778.1|FK345778
EST:     CATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: CATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|18040353|gb|BM308647.1|BM308647
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|254332430|gb|GR843907.1|GR843907
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|207842657|gb|GD815965.1|GD815965
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|209719567|gb|BW651019.1|BW651019
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|193622041|gb|FK570453.1|FK570453
EST:     CAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGCACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: CAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|19934771|gb|BQ079801.1|BQ079801
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... 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|193325608|gb|FK288442.1|FK288442
EST:     CATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: CATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|192307919|gb|FK003067.1|FK003067
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|254348789|gb|GR852468.1|GR852468
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|26047705|gb|CA784416.1|CA784416
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|26045988|gb|CA783372.1|CA783372
EST:     ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGGAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
EST: gi|15203979|gb|BI426756.1|BI426756
EST:     ACCTATATGTTTTCCCCAACTTAAAGTACGTGGGCATTGAATTGTGGCAG                         GTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA
genomic: ACCTATATGTTTTCCCCAACTTGAAGTACGTGGGCATTGAATTGTGGCAGgtaaactttt ... tatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGAT
                         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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacttttcattttaacatcgcaatatttggtttgatacttttggatctgaactctgacaagcaggctattttatcttacagGTGAAATCTGGTACTTTGTTTGACAATGTCTTAATTACTGATGATCCTGAATATGCCAAGCAACTGGCTGAAGAAACATGGGGCAAGCACAAGGAT

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