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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag

Basic information

species Glycine max
transcript GLYMA02G42560.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 21
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgctta-tctcat--gattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag---
  ||||||| || || || || |||||||||||||||||| | || |||||||| || ||||| || ||| |||| || |||||||||||||| ||||| ||||   | |        | | | | ||  || |   ||| | |||  |   ||   ||| ||||   || |     | ||||  |   
GCTGATTAATGTCTGCGACCGCTTTGGATTTGTTCCAGATTTGACCCACTATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAAgtatgcaactcttccaattcagtgttattggagtatcatc-attctcatgtgctatgtatttaaatgcttattttcctttatattgtag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 21
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgctta-tctcat--gattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag---
  ||||||| || || || || |||||||||||||||||| | || |||||||| || ||||| || ||| |||| || |||||||||||||| ||||| ||||   | |        | | | | ||  || |   ||| | |||  |   ||   ||| ||||   || |     | ||||  |   
GCTGATTAATGTCTGCGACCGCTTTGGATTTGTTCCAGATTTGACCCACTATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAAgtatgcaactcttccaattcagtgttattggagtatcatc-attctcatgtgctatgtatttaaattcttattttcctttatattgtag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
lower sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 7
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgct----tatctcatg----attgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag
  ||||||| ||||||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||||| |||| || || |||||||||||||||||||||     ||   |   ||    ||  || ||     || |||   |    ||   | ||   |     || | | |  | || | | |||
ACTGATTAATGTTTGTGATCGCTTTGGTTTTGTGCCAGATCTCACTCACTATCTGTACACAAACAACATGCTTCGATATATCGAAGGCTATGTTCAGAAGgtagttgtgtgtttcgactctgttaattcgtgcgccgttcctaataataggttgaatatgagaacgattaattctttttccttgtttccag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
lower sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 19
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtata---------atagtagct-ttgcttatctcatgattgct-atctactctttt---tctctgcctatctaaaactttgtgcctttctatacag
  ||||||| |||||||| || |||||||||||||||||||| || ||||||||||| |||||||| ||| |||| || ||||| |||||||| || || ||||            |||  || ||  ||    | | |||  | ||||  | |||      | ||  |   |    | || || |||  |||  ||
ACTGATTAATGTTTGTGACCGCTTTGGATTTGTTCCAGATCTGACTCACTATCTATATACAAACAATATGCTTCGGTATATTGAGGGCTATGTACAAAAAgtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttg-tatgtag

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 21
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgcttatctc--atg-attgctatctactctttttctctgcc-tatctaaaactttgtgcctttctatacag
|||||| || || |||||||||||  | ||||| || ||||| || || || || ||||||||||||||| |||| |||||||||||||| || ||||||||||||   |  ||  |  ||  |   |||  |||   |  | | ||||| | ||   ||| || |  ||||   || || |     
TTTGATAAATGTCTGTGATCGTTTCAGCTTTGTGCCTGATCTTACTCATTACCTCTACACAAACAACATGCTTCGTTACATTGAAGGCTACGTGCAGAAGgtataaggtttcctgggactacttttaatgcgttggagttcagtttttttttatgaaatatttatacgtttgattctgtcaaag---

upper sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 21
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 21
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag
||||||||| || |||||||||||||| ||||| || ||||| || || || || ||||||||||||||| | || ||||||||||| || |||||||||||||    |||| ||   |   ||  || |   |||       |||||       |  || |  |  |  || || | ||   
TTTGATTAATGTCTGTGATCGTTTTGGCTTTGTACCTGATCTTACTCATTACCTCTACACAAACAACATGCTGCGTTACATTGAAGGTTACGTTCAGAAGgtat----gtagtttctttagacttttgttaaatatggtaggattttcatgaaagaattatatatgcgatcccttttgtag--

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|209718673|gb|BW662739.1|BW662739
EST:     ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAG                         GTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAA
genomic: ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagt ... ttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAG
EST: gi|209720996|gb|BW682475.1|BW682475
EST:     ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAG                         GTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAA
genomic: ATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagt ... ttctatacagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGATTAACGTTTGTGATCGTTTTGGATTTGTTCCAGATCTAACACACTATCTATACACAAACAACATGGTTCGCTACATTGAAGGCTATGTTCAGAAGgtataatagtagctttgcttatctcatgattgctatctactctttttctctgcctatctaaaactttgtgcctttctatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG