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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtttggtttctctgctcgtggttactgattttttgttgaaaaaaaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG

Basic information

species Glycine max
transcript GLYMA07G33780.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G127948_T04 (Zea mays), 3'ss of exon 4
gtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtt--tggtttctctgctcgtggttactgattttttgttgaaaaaaaaaca-acagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG
                                      || ||      |        |||   |    ||   |   |||  |||  || |||       ||||||||   |   ||||||| | ||||| ||||| || ||||| ||||||||| ||||||||||| | |||||||||   |||||||| |||||||| || || |||||||| || 
------------------------------------gtatgttccgctttcccgggccgatctctcggcggcgacctagctgctgg--acagatcgagatctgaaaaaatggcgtgcagGAACCTGATGACGACCTCCGCCGACGAGGGGCAGTTCCTGAACATGCTCATCAAGCTCATCGGCGCCAAGAAGACCATGGAGATCGGCGTCTACACCGGC

upper sequence: GLYMA07G33780.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0063g00140.t01 (Vitis vinifera), 3'ss of exon 2
gtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtttggtt--tctctgctcgtggttactgattttttgttgaaaaaaaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG
                   |    |||| |  |||   ||| | | | || | ||||    | || |  ||  |   || | ||      |  | ||   |||||||  ||||   |||||||||||||| || ||||| || ||||||||||||||||||||||| || ||||||||||||||||||||||||||||| || || ||||||||||| 
------------------gtgagcttttcttgattcggattctcaaatctttgaatacccgttgtctatttgatgcttgtttgtaac-gttagtgttggtttgaaaacgaaac---agGAACATCATGACTACGTCTGCTGATGAAGGGCAGTTCTTGAACATGCTTCTCAAGCTCATCAATGCCAAGAACACCATGGAGATAGGCGTCTACACTGGC
















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|13311958|gb|BG405609.1|BG405609
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|8403758|gb|BE059325.1|BE059325
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|26048143|gb|CA784719.1|CA784719
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|15661667|gb|BI699038.1|BI699038
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|13312671|gb|BG406322.1|BG406322
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|151395162|gb|EV265033.1|EV265033
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|151401262|gb|EV271076.1|EV271076
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
EST: gi|15000825|gb|BI321639.1|BI321639
EST:     GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATG                         GAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT
genomic: GAACCTGAATCCATGAAAGAACTGAGAGAGTTGACAGCAAAACACCCATGgtatatataa ... aaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttggtttctctgctcgtggttactgattttttgttgaaaaaaaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG
                        tactgat  putative branch site (score: 2)
                             attttttgttgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatataatttatataatttcattttttcaattgacattttgacacctattaatatgattggtttggtttctctgctcgtggttactgattttttgttgaaaaaaaaacaacagGAACATCATGACAACCTCTGCAGACGAAGGGCAGTTCTTGAACATGCTCCTTAAGCTCATCAATGCCAAGAACACCATGGAAATTGGTGTCTACACTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA