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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTATGCTATTGAAAGGTATGATCTCCTTAATGAAATTGTGTTCTTGCAGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaatttttatcctgaaaacgcatctttgaaaattttcttgttaaccaaattttcttacacctccatatgttgaactatttcccag

Basic information

species Glycine max
transcript GLYMA20G23080.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G23080.1 (Glycine max), 5'ss of exon 10
lower sequence: LOC_Os07g14270.2 (Oryza sativa), 5'ss of exon 11
AAGGTATGCTATTGAAAGGTATGATCTCCTTAATGAAATTGTGTTCTTGCAGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattt-ttatcctgaaaacgcatctttgaaaattttcttgttaaccaaattttcttacacctccatat--gt---tgaactatttcccag-------
                                                    | ||||||| | || ||||| ||||| ||||| |||| |||||||||||||||||  ||  ||| | || |      |   |   |  | | |   ||| | | |||     | ||| |  ||   ||  | ||||| | |       
----------------------------------------------------GCTGAGAAGGCTGCTTTTGACGAGGCAGAGAAAAAGAAGGAAGAGGAGgtaaattccttcaccttacaatgttctaatatgaggatgatggatgtacaactgtccttgtcattgcatttcagtctgtgctccatttcactgtctttgc

upper sequence: GLYMA20G23080.1 (Glycine max), 5'ss of exon 10
lower sequence: Vv14s0060g01290.t01 (Vitis vinifera), 5'ss of exon 11
AAGGTATGCTATTGAAAGGTATGATCTCCTTAATGAAATTGTGTTCTTGCAGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaatttttatcctgaaaacgcatctttgaaaattttcttgttaaccaaattttcttacacctccatat-gttgaactatttcccag------------------
                                                    | ||||||| |||||||||| ||||| ||||||||||||||||||||||||     ||| ||  |   |  || ||  |  |||    ||| ||  | ||  | | | |  |    ||  ||| | | |||   ||                  
----------------------------------------------------GCTGAGAAGGCAGCATTTGATGAGGCAGAGAAGAAGAGGGAAGAGGAGgtactaacttaccc--atttcttatattatatgatt----tgtcaattagataatataatatgtatggattattggaatttttggaagttctggttcagtaactgg
















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|31474449|gb|CD416477.1|CD416477
EST:     AGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: AGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|213591613|gb|DB975302.1|DB975302
EST:     GTTGAGAAGACAGCAAGAT-AAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GTTGAGAAGACAGC-ATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|254348440|gb|GR852119.1|GR852119
EST:     GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|9900782|gb|BE609750.1|BE609750
EST:     GTTGAGAAGACAGCATTTGAAGAGGCTGATAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|9440151|gb|BE440661.1|BE440661
EST:     AGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: AGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|10848082|gb|BF070635.1|BF070635
EST:     AGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: AGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|31455934|gb|CD397962.1|CD397962
EST:     AGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: AGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|7285731|gb|AW598218.1|AW598218
EST:     GAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|13482210|gb|BG511553.1|BG511553
EST:     GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|213601764|gb|DB982489.1|DB982489
EST:     GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|254348439|gb|GR852118.1|GR852118
EST:     GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: GTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT
EST: gi|193555675|gb|FK513222.1|FK513222
EST:     AAGAGGGAAGAGGAG                         GAATCAAAGGATGACCCAGTTGACTCTGAT
genomic: AAGAGGGAAGAGGAGgtaaattttt ... tatttcccagGAATCAAAGGATGACCCAGTTGACTCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGTATGCTATTGAAAGGTATGATCTCCTTAATGAAATTGTGTTCTTGCAGGTTGAGAAGACAGCATTTGAAGAGGCTGAGAAGAAGAGGGAAGAGGAGgtaaatttttatcctgaaaacgcatctttgaaaattttcttgttaaccaaattttcttacacctccatatgttgaactatttcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG