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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctattgctttttgtttttttgctccaccctcattgctgtgattgttctgtaaccttttgcttgatttctatgactttgctactgaaaaatatgaag

Basic information

species Glycine max
transcript GLYMA16G09020.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 11
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 5'ss of exon 11
GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctattgctttttgtttttttgctccaccctcattgctgtgattgttctgtaaccttttgcttgatttctatgactttgctactgaaaaatatgaag----
| ||||| ||||| ||||| || || ||||| ||||| || |||||||| |||||| || | || | |||||||||||| ||||| |||||||| || ||||||||     |  | |  ||| |    | |||  |   ||||||   ||||  || |  | ||  || | |  ||  |   |     ||  | | |  |      
GTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGATTGAAAAAAGTGCATCCTATGACGATGTGAAAGCAGCCATCAAgtatgtag---gactatcatttgtcca-tgcacattatctgctgtttctgtttggtcaattgtt--ttaagtcttaaaatgcttgagttggtatacagtagccttc

upper sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 11
lower sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 11
GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctattgctttttgtttttttgctccaccctcattgctgtgattgttctg-taaccttttgcttgatttctatgactttgctactgaaaaatatgaag
| ||||| ||||| ||||| || || ||||| ||||| ||||||||||| |||||| || |||| || || |||||||| ||||| |||||||| || ||||||||  |  |    |   || ||   |||       || | |     | | || ||  ||  ||  |||   | |  || |    |   |  | ||   | 
GCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGATTGAGAAAAACGCCTCCTATGATGATGTGAAAGCAGCCATCAAgtatgtagaa-gtacctcacttgttgcttccgtatggttttcagcttccggtttgctattctgatgagtgaaagc-acaacctcttgataaattagtaatca-

upper sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 11
lower sequence: AT1G79530.1 (Arabidopsis thaliana), 5'ss of exon 11
GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctattgctttttgtttttttgctccaccct-cattgctgtgattgttctgtaaccttttgcttgatttctatgactttgctactgaaaaatatgaag---------
| ||||| |||||||| || ||  | ||||||||||||||||| || ||||| || ||| |||||  ||| || || ||||||||||| ||||| || |||||||  |    | |    |||| |||| | |||    || |   |        | |    |  ||    | |  ||  |   |   |  |   ||| | ||          
GAATGGCCTTCCGTGTACCAACATCGAATGTTTCTGTGGTGGATTTAACTTGTCGACTTGAGAAGGGTGCCTCTTACGAAGATGTTAAGGCAGCCATTAAgtatgctt----cctaaaattttattgcccgaccagatatcgtcatcgaaacattatcgtttaatgtagaactcttaataacctctcatggtttaatgtaaacctctaacag

upper sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 5'ss of exon 11
GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctattgctttttgtttttttgctccaccctcattgctgtg-attgttc-----tgtaaccttttgcttgatttcta--tgactttgctactgaaaaatatgaag----
| ||||| ||||| || || || || ||||| ||||| |||||||| ||||| || |||||||||| |||  | ||||||||||| ||||||||  ||||||||      |   | |   | | |  ||| | |    |  || |  ||  | |     | | |  | |  |   || |  |  | |  || ||  |  ||  |   |      
GAATGGCCTTCCGCGTCCCAACACCTAATGTCTCTGTTGTGGACTTAACTTGTCGACTTAAGAAGAGTGCTACATATGAAGATGTCAAAGCAGCCGTAAAgtatactctctctctctctctctctctctctatctatctatctatctatcatgcccaagtatgatttatcccaaaatattaaaattatctttctctttgaatttccaactaaag

upper sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 11
lower sequence: PP1S309_84V6.1 (Physcomitrella patens), 5'ss of exon 9
GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgta------tgtcta------ttgctttttgtttttttgctccaccctcattgctg--tgattgttctgtaaccttt---tgcttgatttcta-----tgactttgctactgaaaaatatgaag------------------
| ||||| |||||||| |||||||||||||| |||||||||||  |||||   || ||  | ||||  |  || || || ||  | || ||||| || ||||        ||||        |||||| ||     |   | ||     | || ||  |   |||| |  ||  ||    |||    |  | |     || |  ||    ||  |  ||||                     
GTATGGCTTTCCGTGTCCCGACTCCCAATGTGTCTGTGGTGGATCTGACTGTGCGTCTCCAAAAGAGCGGCTCATACGAGGACATCAAGGCAGCCATCAAgtgagggatcgtctgggggtgctgctttgtggcagctgttttcaagtgtagtgatgcttacctgttgttcaagtttgaggtgcccagtaacaagtcgctgccactgacgttgggaggtatggttttgtgcgaatgattgcag

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|254346562|gb|GR856284.1|GR856284
EST:     TGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGA
EST: gi|192334303|gb|FK024402.1|FK024402
EST:     TGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGA
EST: gi|254326011|gb|GR838892.1|GR838892
EST:     TGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAA                         GTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGA
genomic: TGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctat ... aaatatgaagGTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGCTTAAGAAGAATGCATCCTATGAAGATGTTAAAGCAGCAATAAAgtatgtctattgctttttgtttttttgctccaccctcattgctgtgattgttctgtaaccttttgcttgatttctatgactttgctactgaaaaatatgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG