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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttcttttttcttggtatattttttgagggtttctgtcagtttttttttagttgatatatgttagaacttgaggagaaaatttgataattggaa...

Basic information

species Glycine max
transcript GLYMA10G33550.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33550.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM5G804893_T01 (Zea mays), 5'ss of exon 3
AAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgta------atatttcttttttcttggtatattttttgagggtttctgtcagtttttttttagttgata--tatgttagaacttgaggagaaaatttgataattggaa
    || |||||||| |||||| | || ||||||||||| ||  | |||||||||||||||||||| || || ||||||||||||   | ||||||||||||        | |||     ||   ||   |  |  ||       |  || ||    || | | |  ||  | || | |||||| |  |      |||   ||     
----ACCATCAATGGCGACGATCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAAGACTACATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGGTGCgtacggtgtttgggaatttgggggtcaggtcgtgcaatcgccaatctgtcaccttgtcgatcgtacctctgattgaacttaaataatcctgttgggcatc----

upper sequence: GLYMA10G33550.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G064426_T01 (Zea mays), 5'ss of exon 3
AAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgta-atatttcttttttcttggtatattttttgagggtttctgtcagtttttttttagttgatatatgttagaacttgaggagaaaatttgataattggaa----
 ||||| |||||||| |||||  | || ||||||||||| ||  | |||||||| ||||| ||||| || || ||||||||||||   | ||||||||||||   || |  |       | |   | ||      ||||  |   | |  |||  | ||     | ||  |  ||   |   |  |  |||   |||| |     
GAAGACCATCAATGGCGACGACCTGCTGTGGGCCATGGCCACGCTGGGGTTTGAGGACTATATTGAACCCCTCAAGGTGTACCTGCAGAAGTACAGAGAGgtgcgtactgatgaaggtattggggacttc----aggttaattggattgatttggtggtcaggttgtgcaatcacc-aatctgtcaccttgtcgattgtacctct

upper sequence: GLYMA10G33550.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S25_89V6.2 (Physcomitrella patens), 5'ss of exon 3
AAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttcttttttct--tggtatattttttgagggtttct-gtcagtttttttttagttgatatatgttagaacttgaggagaaaatttgataattggaa
|||||| ||||||||||| |||||||| |||||||||   || |||||||||||||||||| | |||||||| ||||| |||||    | ||||||||||||| | |  || || |||  | |    ||| |  ||   | || | | | | | | ||  |   || |  || |               | || |     |||
AAAGACGATCAATGGAGATGATTTACTTTGGGCCATGAGCACATTAGGGTTTGAAGACTACGTCGAGCCGCTGAAGGTTTACCTTCACAAGTACAGAGAGgtactttcgctgttatctgttcgctcctttctcaagacctgcttgactgctctatctttctcc-tacagtttggttacctttattttggtctgct--cccgaa

upper sequence: GLYMA10G33550.1 (Glycine max), 5'ss of exon 2
lower sequence: PP1S25_10V6.1 (Physcomitrella patens), 5'ss of exon 3
AAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttcttttttcttggtat--attttttgagggtttctgtcagtttttttttagttgatatatgttagaacttgaggagaaaatttga-taattggaa
||||||||| ||||||||||||||||| ||||| |||   || |||||||| ||||||||| | || ||||| || || || ||   || ||| ||||||||| | |   |||| |||   ||   | | | | |     |||||   |||  | ||      ||  | |  |    |  |     |  |||| |  ||  ||
AAAGACAATAAATGGAGACGATTTACTGTGGGCTATGAGCACATTAGGGTTCGAAGACTACGTCGAACCGCTAAAAGTTTATCTTCATAAGTATAGAGAGgtattctcgtttttatctatttaaggaatctctcaaatgctctgt---tttcctcttgaaaattaggtttccggttatttgcctgcaccttgagtctttttaa

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|58017783|gb|CX704525.1|CX704525
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG
EST: gi|10845982|gb|BF071234.1|BF071234
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG
EST: gi|33387515|gb|CA850722.1|CA850722
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG
EST: gi|254330848|gb|GR842113.1|GR842113
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG
EST: gi|58021138|gb|CX707880.1|CX707880
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG
EST: gi|208235711|gb|GE031101.1|GE031101
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG
EST: gi|193320720|gb|FK283105.1|FK283105
EST:     TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAG                         GCGGAG
genomic: TTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttc ... gatatcacagGCGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGACAATCAATGGAGACGATTTACTATGGGCCATGGCAACTTTAGGGTTTGAAGACTACATTGAGCCGCTTAAGGTGTACCTGGCTAGGTACAGAGAGgtaatatttcttttttcttggtatattttttgagggtttctgtcagtttttttttagttgatatatgttagaacttgaggagaaaatttgataattggaa

- - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagaaaa