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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGACTATTAACGGCGATGATTTGCTCTGGGCGATGGCCACTCTCGGTTTCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaatttacacaatttcattttctttctttctttttttaatttcaaaagcttttctggcccccggaaacaatattgtctacggtgtgtgattta...

Basic information

species Glycine max
transcript GLYMA03G33490.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G303465_T04 (Zea mays), 5'ss of exon 2
AAAGACTATTAACGGCGATGATTTGCTCTGGGCGATGGCCACTCTCGGTTTCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattt-taatttacaca-atttcattttc--tttctttctttttttaatttcaaaagcttttctggcccccggaaacaatattg-tctacggtgtgtg-attta-----------------------------
|||||| || ||||| || |||||||||||||||||||||||| | || |||||||| ||  | || ||||| || ||||||||    |  |||  |||||| |||  |   |||| |  | |   || |   | |   |||| | |   | | | ||  |||  |    | |    |   | ||  | || |   | || || |                              
AAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCTCTCAAGATTTACCTACAAAAGTACAAAGAGgtcattgatggcttaccctcactgtgttgtagatgtggatcttctctgtttattataatgtttcgtacatctctctcatggtgtttctttatgccctttgcatgttctcttctgatgacgggctggttattacag

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G303465_T02 (Zea mays), 5'ss of exon 3
AAAGACTATTAACGGCGATGATTTGCTCTGGGCGATGGCCACTCTCGGTTTCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattt-taatttacaca-atttcattttctttctttctttttttaattt--caaaagcttttctggcccccggaaacaatattg-tctacggtgtgtgattta
|||||| || ||||| || |||||||||||||||||||||||| | || |||||||| ||  | || ||||| || ||||||||    |  |||  |||||| |||  |   |||| |  | |   || |   | |   | || |   |||   | ||  |||  |    | |    |   | ||  | || |   | ||     
AAAGACAATCAACGGGGACGATTTGCTCTGGGCGATGGCCACTTTAGGATTCGAGGAGTACGTCGAGCCTCTCAAGATTTACCTACAAAAGTACAAAGAGgtcattgatggcttaccctcactgtgttgtagatgtggatcttctctgtttattataatgtttcgtacatctctctcatggtgtttctttatgccctttg-----

upper sequence: GLYMA03G33490.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv08s0040g03260.t01 (Vitis vinifera), 5'ss of exon 2
AAAGACTATTAACGGCGATGATTTGCTCTGGGCGATGGCCACTCTCGGTTTCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaatttacacaatttcattttctttctttctttttttaatttcaaaagcttttctggcccccggaaacaatattgtctacggtgtgtgattta--
 ||||||||||| || ||||||||||||||||| ||||| ||| | || || ||||||||||| ||||| || ||  | ||| |  ||  |||| |||||||||| |   |||  ||  |    ||||||   ||| |||     |||     || || | ||   | | |||   ||   || |    ||| |  ||    
GAAGACTATTAATGGGGATGATTTGCTCTGGGCAATGGCGACTTTAGGGTTTGAGGATTATATTGATCCGCTGAAGTTGTACTTGGCTGCATACAGAGAGgtaatatgtctttg-actttcgggttttctcgatttgtttagaccattgatgtag-ttgtttgcttcactgaattgatgccgttttttttgtcttgttattc

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|14011130|gb|BG726061.1|BG726061
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|8826311|gb|BE210041.1|BE210041
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|21677121|gb|BQ629472.1|BQ629472
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|5605926|gb|AI900024.1|AI900024
EST:     TCGAGGATTATATGGATCCTCTTANAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|298195680|gb|HO044071.1|HO044071
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAGGGTGATAC
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAGGGTGATAC
EST: gi|16346723|gb|BI972318.1|BI972318
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|7285143|gb|AW597630.1|AW597630
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|5761187|gb|AI966550.1|AI966550
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|18730588|gb|BM525962.1|BM525962
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|7029546|gb|AW459387.1|AW459387
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|8284382|gb|BE021941.1|BE021941
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG
EST: gi|14991093|gb|BI316766.1|BI316766
EST:     TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAG                         ATGGAG
genomic: TCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaa ... aatgttacagATGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGACTATTAACGGCGATGATTTGCTCTGGGCGATGGCCACTCTCGGTTTCGAGGATTATATGGATCCTCTTAAAATTTACCTCACTAGATACCGAGAGgtaattttaatttacacaatttcattttctttctttctttttttaatttcaaaagcttttctggcccccggaaacaatattgtctacggtgtgtgattta

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccgg