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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttatattttatcatgacatacttttattctttgaaaccttctgttgtttgatttgttggagaaattgacaacc...

Basic information

species Glycine max
transcript GLYMA01G03610.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os05g16660.1 (Oryza sativa), 5'ss of exon 6
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttatattttatca-tgacatacttttattctttgaaaccttctgt-tgtttgatttgttggagaaattg-acaacc---
||| | ||||| |||||||| ||||||||||| ||||||||||||||||| ||| |||| ||||| |||||||||   |||||       | ||||| |      | | ||||| ||| | ||  ||| || | ||||   |   |   | | |  | |||| | |       |   |  ||    
ATTTTGCAAGAGGAAATTGGTGGTGTAAAAGGCCATTTTGGACCAATTAACGCACTGGCATTTAATCCTGATGGACGGAGgta------atattcttaatacatgtgtaatattatatgaatgctatatttatgttctaccaccgcacttatgttctcgattagctttttgtttcatattactttg

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os08g21660.2 (Oryza sativa), 5'ss of exon 6
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgta-tattctgtgttcttcaactcccttttatattttatcatgacatac-ttttattctttgaaaccttctgttgtttgatttgttggagaaattgacaacc
||| | ||||| |||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||||| ||||||||    ||||| ||||||   | | |  | |    ||||  || |  |    ||    | || ||  ||      |||   | ||||  |  ||   |   |  |  |  
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGCCATTTTGGACCAATTAACGCGCTGGCATTTAATCCTGATGGGCGGAGgtaatattcttaatacatgtatttgtatttacgttctgcccctgcacttatgttcttgattagctttttcccatatttgtgtgctttttgc--tcaatgatt

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G143330_T01 (Zea mays), 5'ss of exon 6
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttatattttatcatgac--atacttttattctttgaaaccttctgttgtttg-atttgttggagaaattgacaacc
||| | ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| ||||| ||||||||    |||||  || | |  |||   | |   | |    ||   ||||      || | |||    ||||  |    | |||     || || ||     ||||   |  
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGGCATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaatttttttaatctgacagtggttgtctctttcagtcatagttggtagtattaacagttgac-caggttattgcccatatatgctgtttttattgtata--

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G028834_T03 (Zea mays), 5'ss of exon 6
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgta-tattctgtgttcttcaactcccttttatatttta-tcatgaca--tacttttattctttgaaaccttctgttgtttgat-ttgttggagaaattgacaacc
||| | ||||| |||||||| ||||| ||||| |||||||| ||||||||||| ||||| ||||| ||||||||    ||||| || | | | || ||  |||    ||| | || || |||| |    || ||| ||| | | || | ||  |    || |  ||||   |    |   |    
ATTTTGCAAGAGGAAATTGGTGGTGTTAAAGGACATTTTGGGCCAATTAATGCTTTGGCATTTAATCCTGATGGGCGGAGgtaataattttttttatttgactgtggttttttttgtagtcattattgttagtttcattgtatcaa-catttggccacttaacattgtctaaaggttatgc----

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: AT2G46290.1 (Arabidopsis thaliana), 5'ss of exon 8
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatatt--ctgtgttc---ttcaactcccttttatattttatcatgacatacttttattctttgaaaccttctgttgtttgatttgttggagaaattgacaacc
||||| ||||| |||||||| || || ||||| ||||||||||| |||||||| ||||| || |  |||||||| || ||||| | |  |    ||    ||  | |   |  || | |   |||    ||     | || |||      |  || ||  || ||| | | |   |||  ||   
ATTCTGCAAGAGGAAATTGGTGGCGTGAAAGGTCATTTTGGACCTATTAATGCTTTGGCATTCAGTCCTGATGGGAAGAGgtaaactaacaaaatttgattttgattgattgatacaatcc-tcagttgatgagagtgttttttaggctttgttgctgagtgttttttggaatgtattttcag--

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: AT2G46280.3 (Arabidopsis thaliana), 5'ss of exon 6
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttat--attttatcatgacatacttttattctt--tgaaaccttctgttgtttgattt-gttggagaaattgacaacc---
||||| ||||| |||||||| ||||| ||||| ||||||||||| || ||||| ||||| || || |||||||| || ||||| |||        ||  | |    || ||  |    ||| | ||||  |    || |   ||     ||  | | | | | |  ||| | | |||  | |      
ATTCTGCAAGAGGAAATTGGTGGTGTGAAAGGTCATTTTGGACCTATAAATGCTTTGGCATTCAATCCTGATGGGAAGAGgtaaattaacaacatttggattttgattgattgacacaatcctcacatgatgaggttttgagtgtgtgttttggctctctcactgagtttgtggaatgtatatttcag

upper sequence: GLYMA01G03610.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv01s0011g06630.t01 (Vitis vinifera), 5'ss of exon 7
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttctt-caactcccttttat--attttatcatgacatacttttattctttgaaaccttctgttgtttgattt-gttggagaaattgacaacc
|||||||||||||||||||| ||||| |||||||| |||||||| || ||||| || || || |||||||||||||| ||||| | | | |  | ||    |    | ||    |||   |      | || || ||      || |      || |   |||| | | || | |    |    
ATTCTTCAAGAAGAAATTGGAGGTGTGAAAGGGCACTTTGGACCTATAAATGCTTTAGCATTCAACCCTGATGGAAAGAGgtacactttcttctattatggcatgttattgctgattaagtttcttaaaacattgatgagcaaaagctccacattttcaaatttaggttgaaacaccctc----

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|208323562|gb|GE119179.1|GE119179
EST:     TTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTCGACCC
genomic: TTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|193383818|gb|FK353015.1|FK353015
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTT-CAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGAACC
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGA-CC
EST: gi|213604401|gb|DB983489.1|DB983489
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|209726208|gb|BW659573.1|BW659573
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|193449022|gb|FK413817.1|FK413817
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTT
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTT
EST: gi|193552832|gb|FK510723.1|FK510723
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTT
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTT
EST: gi|208073965|gb|GD871550.1|GD871550
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|15662606|gb|BI699977.1|BI699977
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|193312788|gb|FK280856.1|FK280856
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|208111164|gb|GD910030.1|GD910030
EST:     TTTTGGACCAATTAATGCATTGGC--TTAACCCTGATGGAAAAAG                         TTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
genomic: TTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGGAGGTGAAGATGGTTATGTACGGTTGCACCACTTTGACCC
EST: gi|207774007|gb|GD745523.1|GD745523
EST:     GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAG                         TTTTTCAAGTGG
genomic: GGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctg ... tcttgtgtagTTTTTCAAGTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTTCAAGAAGAAATTGGGGGTGTAAAAGGGCATTTTGGACCAATTAATGCATTGGCTTTTAACCCTGATGGAAAAAGgtatattctgtgttcttcaactcccttttatattttatcatgacatacttttattctttgaaaccttctgttgtttgatttgttggagaaattgacaacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA