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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagttttaatgtctgtaatcttttatgacccatcaaaatccatgggcttgttagtggtgatattgagttttggcatgcag

Basic information

species Glycine max
transcript GLYMA19G36860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G36860.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G03430.1 (Arabidopsis thaliana), 5'ss of exon 3
TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagttttaatgtct-----------gtaatcttttatgacccatcaaaat-------ccatgggcttgttagtggtgatattgagttttggcatgcag
|||||| ||||| ||||| ||||||||||||||||| || || || |||||||  ||    |           ||   |||||  ||    |     |       |||  |  |  | |||  | ||| ||| |  ||   |  ||
TATTGAAGAGGTCGCCTTTAGTTTCAATGGAGGAAAAGACTCCACTgtaagttacaactcttcccttccaaaagtctcctttttggatgttttctttttttccccccactgtttcctaagtaataataatgactcatgattt-tag

upper sequence: GLYMA19G36860.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 5'ss of exon 3
TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagttttaatgtctgtaatcttttatgacccatcaaa-atccatgg--gcttgttagtggtgatattgagttttggcatgcag-------------------
| |||| ||||||||||| || ||||||||||||||||||||||| || |||| | || | |||  ||||  ||  | |||   | |||  |    |||| |   | |   |||||| | ||    |||                     
TGTTGAAGAGGTTGCCTTAAGCTTCAATGGAGGAAAGGATTCAACTgtgagttcttatatttgttttcttcaatatctcattgcatatctctcaatgcttatcttttgccttattgattgtttttctgccaatgaactggggttttgcag
















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|14258476|gb|BG881384.1|BG881384
EST:     TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACA                         GTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCATAAAAAGGGGCAA
genomic: TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagtttta ... tggcatgcagGTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
EST: gi|7691690|gb|AW759813.1|AW759813
EST:     TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG                         GTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
genomic: TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagtttta ... tggcatgcagGTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
EST: gi|209709323|gb|BW680988.1|BW680988
EST:     TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG                         GTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
genomic: TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagtttta ... tggcatgcagGTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
EST: gi|192299088|gb|FG990402.1|FG990402
EST:     TATGGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG                         GTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
genomic: TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagtttta ... tggcatgcagGTTTTGTTGCACATACTCAGGGCTGGCTATTTCTTGCACAAAAAGGGGCAA
EST: gi|213614119|gb|DB964891.1|DB964891
EST:     TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACG                         GTTTTGTTGCACATACTCAGGGCTG
genomic: TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagtttta ... tggcatgcagGTTTTGTTGCACATACTCAGGGCTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGAGGAGGTTGCCTTCAGTTTCAATGGAGGAAAGGATTCAACGgtaagttttaatgtctgtaatcttttatgacccatcaaaatccatgggcttgttagtggtgatattgagttttggcatgcag

- - GAGGAG
- - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - GGAGGA