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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCTTAAAGACAGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtacttgctgcaaaagtctgtttctgttcatatataatttgggtttgtatgtctggttttaaatctagtttggcactcaattttcacatgaatgtg...

Basic information

species Glycine max
transcript GLYMA15G07570.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G07570.3 (Glycine max), 5'ss of exon 6
lower sequence: AT1G61150.3 (Arabidopsis thaliana), 5'ss of exon 5
TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCTTAAAGACAGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtacttgctgcaaaagtctgttt--ctgttcatatataatttgggtttgtatgtctggttttaaatctagtttggcactcaattttcacatgaatgtg
|||| ||| || |||  |||||| |||||  | || || ||  | |||||||||||||| || |||||||| || ||||| ||||||||||| |||||||||   |  |   |    | ||     |   |||   |   ||         |     | |  | |  |   |  ||    | ||||| || | ||  |    
TCTACCTGCCCGGTTAAAGAGCTTCTTGATCTTTCCCACCGTCTTAAGACAGCAAGTGAAGTAAATGCAGCGATTCTTACAAGCCAGAGCCACGAAAAAGgtagcttttgaattttgatgttatactggttgtcttttagtagccacaaaataccattataatctcgagcatcattcatta-tcaatcttaagattcaaag-

upper sequence: GLYMA15G07570.3 (Glycine max), 5'ss of exon 6
lower sequence: Vv10s0116g00670.t01 (Vitis vinifera), 5'ss of exon 11
TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCTTAAAGACAGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtacttgctgcaaaagtctgtttctgttcatatataatttgggtttgtatgtctggttttaaatctagtttggcactcaattttcacatgaatgtg---
|||||||| |||||||| || || || ||||||||||| ||| | ||||||||||| |||||||||||||| || ||||| |||||||| |||||||| |||| ||  |   | |     |   |      || |  ||  |    ||||| ||||   | |  | |  |  |||    |       || ||   || ||   
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctc--agtttgaatgtgccgctcaacagtttctttactgcatggcagtcgca-atatatggaa

upper sequence: GLYMA15G07570.3 (Glycine max), 5'ss of exon 6
lower sequence: Vv00s0445g00060.t01 (Vitis vinifera), 5'ss of exon 2
TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCTTAAAGACAGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtacttgctgcaaaagtctgtttctgttcatatataatttgggtttgtatgtctggttttaaatctagtttggcactcaattttcacatgaatgtg---
|||||||| |||||||| || || || ||||||||||| ||| | ||||||||||| |||||||||||||| || ||||| |||||||| |||||||| |||| ||  |   | |     |   |      || |  ||  |    ||||| ||||   | |  | |  |  |||  | |       |  ||   || ||   
TCTAACTGCCCTGTTGGTGAACTCCTGGACATATCACAACGCCTGAAGACAGCAAGCGAGGTGAATGCAGCCATCCTTACAAGCCAGAGTCATGAAAAGGgttagtcttctttccttctataaatacagcatcttggatgctc--agtttgaatgtgccgctcaacagtttctttaccgcgtggcagttgca-atatatggaa

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|193499523|gb|FK461276.1|FK461276
EST:     AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAG                         ACCCTAAACTTCCAAGCTTGTTGAAGATGCTGCTA
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTA
EST: gi|38193470|gb|CF922676.1|CF922676
EST:     AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAG                         ACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
EST: gi|16348257|gb|BI973852.1|BI973852
EST:     AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAG                         ACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
EST: gi|58021979|gb|CX708720.1|CX708720
EST:     AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAG                         ACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
EST: gi|192328969|gb|FK021072.1|FK021072
EST:     AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAG                         ACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
EST: gi|22928038|gb|BU545177.1|BU545177
EST:     AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAG                         ACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATGCGCCCAAAACCAGC
EST: gi|151408269|gb|EV278077.1|EV278077
EST:     AGCAAGTGAG-TGAATGCAGTTATACTTACTAGCCAGAGCCATGAAAA-G                         ACCCAAA-CTTCCA-GCTTGTTGAAGATGCTGCTATG
genomic: AGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtactt ... tttttggcagACCCAAAACTTCCAAGCTTGTTGAAGATGCTGCTATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTAACTGTCCTGTTGGAGAGCTGCTTGACATATCACAGCGCTTAAAGACAGCAAGTGAGGTGAATGCAGCTATACTTACTAGCCAGAGCCATGAAAAAGgtttgtacttgctgcaaaagtctgtttctgttcatatataatttgggtttgtatgtctggttttaaatctagtttggcactcaattttcacatgaatgtg

- - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT