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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagactattccatgtataatcttcttctgtacttgcctcttgtctttgagttgatggcttgaagatttatgtgcttattttttaggcataaccaaa...

Basic information

species Glycine max
transcript GLYMA10G42940.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42940.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G181151_T02 (Zea mays), 5'ss of exon 4
GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagactattccatgtataatcttcttct-gtacttgcctcttgtctttgagttgatggcttga-------agatttatgtgcttattttttaggca--taaccaaa---------------
|| || || |  ||||| ||||| || || ||  | |||||||| || ||||| ||||| ||||| || || |||||||| |||||||||||||| |||||||        |     |||  |||| |  | ||| || |   |||   |||| || |  |  ||        || | ||| | || |    ||||     |||  ||                
GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCACTCGCCGTGGTCAAGTCCTTGAAGTTGATGGAGAAAAAGCTGTTGTGCAGgttacttctccattgccttattgtcttttagtagtagttccaaattgatgttgattttacagtatggttaggctaggtctatttcctgaaaacttagtttgttaattaactgcattattcatcag

upper sequence: GLYMA10G42940.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G094497_T02 (Zea mays), 5'ss of exon 3
GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagaga-ctattc-catgtataatcttcttctgtacttgcctcttgtctttgagttgatggcttgaagat-ttatgtgcttattttttaggcataaccaaa-----------------------
               || ||||| || || ||  | |||||||| || | ||| ||||| ||||| || || |||||||| |||||||||||||| |||||||     | |||| | ||  |  | ||   | ||| ||     |||  ||||| |     |  ||   || |||  | | |       |  | ||                             
---------------GAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAGgttacttctccattctcctgattgttttttagcagtagttctaatttgattttgattctgcagtatggtcatgttagttccattcccagaaaacttagtttgttaattaactgcattattcatcag

upper sequence: GLYMA10G42940.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G094497_T01 (Zea mays), 5'ss of exon 4
GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagaga-ctattc-catgtataatcttcttctgtacttgcctcttgtctttgagttgatggcttgaagat-ttatgtgcttattttttaggcataaccaaa-----------------------
|| || || |  ||||| ||||| || || ||  | |||||||| || | ||| ||||| ||||| || || |||||||| |||||||||||||| |||||||     | |||| | ||  |  | ||   | ||| ||     |||  ||||| |     |  ||   || |||  | | |       |  | ||                             
GGCCCAAAGTACCAAGAAATTGTAAACATCCGACTTGGAGATGGCACCAATCGCCGTGGTCAAGTCCTGGAAGTTGATGGCGAAAAAGCTGTTGTGCAGgttacttctccattctcctgattgttttttagcagtagttctaatttgattttgattctgcagtatggtcatgttagttccattcccagaaaacttagtttgttaattaactgcattattcatcag

upper sequence: GLYMA10G42940.3 (Glycine max), 5'ss of exon 4
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 5'ss of exon 5
GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgtta---gagacta--ttccatgtataatcttcttctgtacttgcctc----ttgtctttgagttgatggc--ttgaagatttatgtgcttattttttaggcataaccaaa-----------------------------------------
|| || ||||  ||||| ||||| ||||| ||| | || ||||||||||| || ||||| |||||||| || |||||||| || ||||||||||||||||||    ||  ||   |  | | | || | |||| ||   |||| |||    |||    | | ||||  ||  ||| | ||  ||||  |  ||   ||| ||| |  |                                           
GGGCCTAAATACCAAGAAATTGTCAATATCCGTCTTGGGGATGGAACTACCCGACGTGGTCAAGTTCTCGAAGTTGATGGAGAGAAAGCTGTTGTTCAGgtttcttgaatcttcctctcttctttagttttctgctcctcttgtctccactttgatgcttaattgaacgcatttgtaaatcaatgtaatc-ttgcatagtcattattattcaacacactgcgaggtaaatttctttgatttgcttgtccag

upper sequence: GLYMA10G42940.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 5'ss of exon 4
GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagactattccatgtataatcttcttctgtacttgcctcttgtctttgagttgatggct-tgaagatttatgtgcttat---tttttaggcata-accaaa---
|||||||||| |||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||||||||| ||||| ||||| |||||    || || |    || |  | |||| |  ||  |||   || | ||  |||| |||  | |  |   |||  || ||     ||||||  ||   | || |   
GGACCCAAATATCAAGAGATTGTCAATATTCGTTTGGGAGATGGAACAACTCGACGTGGTCAAGTCCTAGAAGTTGATGGTGAGAAAGCAGTTGTGCAGgt----gattact----gtttggtattctccattatgtgctcatttttttgaagttcatgattatacattcttaaatggtttcatatttttaaacacctatcacattt

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|120533616|gb|EH261749.1|EH261749
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|120533425|gb|EH261558.1|EH261558
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|209697688|gb|BW655589.1|BW655589
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|120533188|gb|EH261321.1|EH261321
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|13478635|gb|BG508033.1|BG508033
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|120532915|gb|EH261048.1|EH261048
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|120533316|gb|EH261449.1|EH261449
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|213596831|gb|DB964094.1|DB964094
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|120533627|gb|EH261760.1|EH261760
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|213591852|gb|DB973417.1|DB973417
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|19053577|gb|BM732244.1|BM732244
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|16346337|gb|BI971932.1|BI971932
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|209727398|gb|BW669851.1|BW669851
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|208145241|gb|GD941760.1|GD941760
EST:     GAAAAGGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCGATTT
genomic: GAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|120533687|gb|EH261820.1|EH261820
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
EST: gi|213595962|gb|DB955998.1|DB955998
EST:     CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAG                         GTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT
genomic: CTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagact ... tattgaccagGTATTTGAAGGTACATCTGGAATCGACAATAAATTTACGACTGTGCAATTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACCCAAATTTCAAGAGATTGTTAATATTCGTTTAGGAGATGGAACTACTCGGCGTGGACAAGTTCTAGAGGTTGATGGTGAAAAAGCTGTTGTTCAGgttagagactattccatgtataatcttcttctgtacttgcctcttgtctttgagttgatggcttgaagatttatgtgcttattttttaggcataaccaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT