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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttaaaccttaaaattattctattgagcaactgttctattcttcagagattaaaaaggctatctatattgttgtgattttttttcttttcttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT

Basic information

species Glycine max
transcript GLYMA11G11960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 2
lower sequence: AT4G34640.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------gtttaaaccttaaaattattctat--tgagcaactgttctattcttcagagattaaa----aaggctatctatattgtt-gtgattttttttct---------tttcttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT
                                  || | ||  | |   |  || |   |  || |   |||| || |  |  | ||  |    |  || |||| | || || ||| || |  | ||         |||  |  ||||||||||||||||||||||  ||| ||||  ||||| || || |||||||| |||||||| || || || |||  ||||||||| | |||||
gttagtgtctcttaactttgctttcaagattaccttgatacgatgaggcttctccaaaatctgctatatttctgttttgaaatgcttttatgttagagccatctttcttcttcgtgcttctgctgctaatattattttttgtacgacagAGGATGATACTAGCATACCAACTGATGAAAAGGTTCCCATCCTGATAGCTTTTCACCGGCACATATACGATACTGATTGGCATTATTCAT

upper sequence: GLYMA11G11960.3 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g00450.t01 (Vitis vinifera), 3'ss of exon 2
gtttaaaccttaaaattattctattgagcaactgttctattcttcagagattaaaaaggctatctatattg----ttgtgattttttttcttttcttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT
  |   |  | |||||| | || ||         ||  | |  |   |  |||  |||   || |||  |     |  | |||  | |    ||||||| |||||||||||||| |||||    ||||||||||| ||||| || |||||||| ||||| |||||||| ||||| ||||| ||||| ||| |||
--tgttatttcaaaatt-tcctgttatctcttactttcagttatactatgttactaagtggatatatgctcaccctcctaattcatctatggttctttt-acagAGGATGATACAAGCATTCGTACAGATGTCAAAGTGCCTATTCTGATAGCTTTTCATCGTCATATATATGACCGTGACTGGCATTTTGCAT
















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|209703098|gb|BW673283.1|BW673283
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|10709996|gb|BF009720.1|BF009720
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGGTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|209722769|gb|BW682867.1|BW682867
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|8826251|gb|BE209981.1|BE209981
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTTCAAG
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGT-CAAG
EST: gi|27446333|gb|CA953456.1|CA953456
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|20813646|gb|BQ298124.1|BQ298124
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|209725283|gb|BW672760.1|BW672760
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|193499460|gb|FK461255.1|FK461255
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|213595316|gb|DB968448.1|DB968448
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
EST: gi|209714966|gb|BW650812.1|BW650812
EST:     GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTG                         AGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT
genomic: GTTTGCATATTTTATTTGGTTCTGCGAGCTCTCGACACCGTTGgtttgtattc ... cttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagattaaaaaggctatctatattgttgtgattttttttcttttcttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT
                       ttgttgtgattttttt  CT-rich tract
                   tatattgttgtgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaaaccttaaaattattctattgagcaactgttctattcttcagagattaaaaaggctatctatattgttgtgattttttttcttttcttttgacagAGGATGATACTAGCATAGAAACAGATGTCAAGGTGCCAATACTGATAGCCTTTCACCGTCATATTTATGATCGTGATTGGCACTTTTCAT

- - - - - - - - - - - - - -gcaactg
- - - - - - - - - - - - - - - - - - - - - - - - -attaaaaa