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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatctaactgcttagagttaagattttatctatttgtcttgcaattggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG

Basic information

species Glycine max
transcript GLYMA04G39520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 2
----aaatctaactgcttagagttaagattttatctatttgtcttgcaattggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG
       |    ||  || |||| || |  |   ||      | |  | |||||   |  |     ||  | | ||   ||||     | || ||| | |||||||||| || |||||||||||||| |||||||| ||||||||  ||||||| ||| ||||| ||   || || ||||| ||||   | |||||||| ||||
tatttgctggccctttttggagtaaaaaagtg--ctgccatacctttatttggtg--atcatttctatgggttgctatttcatggttattttatttttgcacagGCTGTAACTGCAATGGTCCAGCAAGCTATGCAGTATATTGACCAGACACCGGATATTGAATCTAAGATTGAGCTCATTAAAACACTTAACAGTGTGTCTG

upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 2
---aaatctaactgcttagagttaagattttatctatttgtcttgcaattggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG
    |   ||| ||||||   ||  |   | | | |  |   |  || ||        |  ||| |   || |       ||     |  |  |  ||  ||||||||||| || ||||| ||||| |||||||| ||||||||||| || |||||  | |||||||| || ||  | ||  | |   | |||| ||||||||
cctcacattaattgcttattatttgg-cgtcagcgagctcattgtcacttctcgattcagtcataa--cgaactaaaggtatggcattgatgatgatatgcagGCTGTGACTGCGATGGTGCAGCAAGCTATGCAGTATATTGATGAAACTCCAGACGTAGAAACTCGAATTGAGTTGATTCAGACTCTCAACACTGTATCTG

upper sequence: GLYMA04G39520.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 2
aaatctaactgct-tagagttaa--gattttatctatttgtcttgcaattggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG
   |    | ||  | || | ||  |||| ||  |       | || | || ||     ||  | | |||  | |      | |     ||     |   ||||| |||||  ||||||| ||||| |||||||| ||||| ||||| || |||||| ||||||||||||| | ||| ||| | |   | |||| ||| || |
--gtgaggcagccctcgaataaatcgattgtacatgagatggtagccactgctaggcttaatctca-atggacttaagctgtgacttctttggagatttgcagGCCGTGACTTCAATGGTGCAGCAAGCTATGCAGTATATAGATGAAACTCCAGATGTTGAAACTCGTATTGCACTGATCGAGACTCTCAACACTGTGTCCG

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|208154368|gb|GD952663.1|GD952663
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|193450548|gb|FK412990.1|FK412990
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGG
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGG
EST: gi|193625139|gb|FK575671.1|FK575671
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|207815517|gb|GD788682.1|GD788682
EST:     TTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|20812745|gb|BQ297231.1|BQ297231
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|20207825|gb|BQ133914.1|BQ133914
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|15284713|gb|BI468604.1|BI468604
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|208274130|gb|GE071500.1|GE071500
EST:     CAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: CAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|192297411|gb|FG990689.1|FG990689
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|208065744|gb|GD864311.1|GD864311
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|207780366|gb|GD752175.1|GD752175
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|207697727|gb|GD681212.1|GD681212
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|7478560|gb|AW666314.1|AW666314
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
EST: gi|11274759|gb|BF325094.1|BF325094
EST:     TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAG                         GCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA
genomic: TCAATGACCAGATTGTTCTCTTGTCCAAACGCCGTGGCCAGCTTAAGCAGgtaatggctc ... ttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG
                                     cctattcttt  CT-rich tract
                                       tattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatctaactgcttagagttaagattttatctatttgtcttgcaattggtacaagaaacatgatatgatccttcatcataagcctattctttgtacacagGCTGTGACAGCAATGGTCCAGCAGGCTATGCAATATATTGATGAGACACCAGATCTTGAAACTCGTATAGAACTCATCAAAATCTTGAACAGTGTATCTG

- - - -actgctt
- - - - - - - - - - - - - - - - - - - cttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatatg