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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttggcctatttcatagtagatacaattcaaccacctttaaccctaggttaaaagttgtgcattttttttttaaaattgcatattgtttttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA

Basic information

species Glycine max
transcript GLYMA20G03210.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G03210.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g17650.1 (Oryza sativa), 3'ss of exon 3
-------atttggc-ctatttcatagtagatacaattcaaccacctttaacc--ctaggttaaaagttgtgcattttttttttaaaattgcatattgtttttccatg-cagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA
       ||| | | |||     ||  | | | | |  ||  |  | || |    |   || |  |   |  | ||||    | |   ||| | |  | |    ||  ||||||||||| || || |||   |||||||| |||||||| |||||||| || ||||| |||||| ||||||| || |
gtagacaattggacactacactctaacacagaaagtgaaagtatatctatctattttttttgatcgagttcaaattttgagattactgtgcttgtcatatcaatatttcagGAAGATATTCAGCTTATGGCAGACATGGGGATGGATGCATATAGATTCTCAATTTCATGGTCTAGGATTTTCCCAA

upper sequence: GLYMA20G03210.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G26560.1 (Arabidopsis thaliana), 3'ss of exon 2
atttggccta--tttcatagtagatacaattcaaccacctttaaccctaggtt---aaaagttgtgcattttttttttaaaattgcatattgtttttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA
 |    || |  ||  ||| || ||  ||   ||    |  |||   ||  ||   |||| ||    | |    |||| |  ||| | ||| |  |     |||||||||| ||||||| |||||| | ||||||||||| || || |||||||||||||||||| | || || ||||| |
gtaaaccccaatttctataataaat-taacaaaatggtcaataagtatacatttcgaaaatttaattaatgaagttttga--ttgga-attatggtgatg-gcagGAAGATGTACAACTTATGAAGAATATGGGAATGGACGCTTACAGATTTTCCATTTCTTGGACCCGCATCTTTCCAA

upper sequence: GLYMA20G03210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g00750.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------------------------------atttggcctatttcatagt--agatacaattcaaccacctttaaccctaggttaaaagttgtgcatttttttttta---aaattgcatattgtttttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA
                                                                                 |||| |    ||| | |||  | ||  |||  |  |||        ||    ||  | || | ||| |||| | ||   ||||| |||  | | ||    | ||||| ||| ||||||| |||||| ||||||||||||||||||| ||||||||||| || ||||| |||||||| ||  
gtaagccccattcatatcgattccaattcggttttcttttaccaagagatccagttgacattatctcaccttactataaatattttgtaacttttacagtcaaaatttaatgta-tcacacagccttctgcagtatcatttcttcatcttttgtgtacttaaatttcatggt-tgttgtattccagGATGATGTACAACTCATGAAGAACATGGGAATGGATGCCTACAGATTTTCCATATCCTGGTCCCGGATTTTCCCTG

upper sequence: GLYMA20G03210.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0011g00760.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------------------------------------atttggcctatttcatagt--agatacaattcaaccacctttaaccctaggttaaaagttgtgcatttttttttta---aaattgcatattgtttttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA
                                                                                |||| |    ||| | |||  | ||  |||  |  |||         |    ||  | || | ||| |||| | ||   ||||| |||  || || |   | ||||| ||||||||||| |||||| ||||||||||||||||||| ||||||||||| || ||||| |||||||| ||  
gtaagcccattcatacccattccaattcggttttcttttaccaagagatccagttgacattatctcaccttactatagatattttgtaacttttacagtcaaaatttaatgta-tcacacagccttttgcagtatcatttcttcatcttttgtgtacttaaatttcatggtggttgtat-tccagGATGATATACAACTCATGAAGAACATGGGAATGGATGCCTACAGATTTTCCATATCCTGGTCCCGGATTTTCCCTG

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|254348672|gb|GR852351.1|GR852351
EST:     TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAA                         GAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC
genomic: TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAAgtaagtaaca ... ttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC
EST: gi|7588722|gb|AW704511.1|AW704511
EST:     TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAT                         GAAGATATACAACTGATGAATGACATGGGAATGGATGCCTATAGATTTTCC
genomic: TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAAgtaagtaaca ... ttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC
EST: gi|11689544|gb|BF597220.1|BF597220
EST:     TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAA                         GAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC
genomic: TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAAgtaagtaaca ... ttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC
EST: gi|254326998|gb|GR836607.1|GR836607
EST:     TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAA                         GAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC
genomic: TTGATTTCAGCAATGCTGATGTTGCGGTGGATCAGTACCACCGATACGAAgtaagtaaca ... ttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggttaaaagttgtgcattttttttttaaaattgcatattgtttttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA
                                       ttgtttttcc  CT-rich tract
                 attttttttttaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttggcctatttcatagtagatacaattcaaccacctttaaccctaggttaaaagttgtgcattttttttttaaaattgcatattgtttttccatgcagGAAGATATACAACTGATGAAGGACATGGGAATGGATGCCTATAGATTTTCCATTTCTTGGTCTCGGATTTTTCCCA

- - - - - - - - - - - - caattca
- - - - - - - - - - - - - - - - ccacctt
- - - - - - - - - - - - - - - - - - - - -accctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatat