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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc...

Basic information

species Glycine max
transcript GLYMA01G43470.4
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: LOC_Os01g48910.2 (Oryza sativa), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaag--ttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc-
 |  || ||||| || ||  || | ||||| || ||||| |||||||| || || ||||| |||||||||||| |||||||| |||| ||||| || ||||||  |    |   ||| | |||    |||| || |    |  | || ||  ||  ||||  |  ||||  ||  |     |     ||  ||||    |   
CAGGGCTGTTCATCTGGAGCCAGTGCCATTCGATATGGATCGTGACCTAATTACCCCAACTTACAAGAAGAAGCGGCCACAGCTGCTCAAATATTACCAGgtaagaacactagaaaaatatcttc-ctgcaatttaaggtacttggattatcatccgtctaaatctgga--actctgtccgacaatctgccatttttttttag

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: GRMZM2G152127_T01 (Zea mays), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcact--tcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
 |  || ||||| || ||| |    || || |||||||| || ||||||||||| || || |||||||||||| |||||||| |||| ||| |||||||||||        ||  |||     | |   ||   ||    |  | |   |   | |  |||   ||  ||    ||      |    ||             
CAGGGCTGTTCATCTGGACCCCGCACCGTTCGACATGGAGCGCGACCTTATCACCCCGACGTACAAGAAGAAGCGGCCACAGCTGCTGAAACACTATCAGgtatgg--cagcagtttcagataactcgcttgggctaacgacgtcggtgaagcttgaccttcgtgttaatgtttttgtcgcttttcgtgcag----------

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: AT4G11030.1 (Arabidopsis thaliana), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
|||||  ||||| || ||  || |  | || ||||||||||| |||||| | |||||||| ||||| ||||||||||| || ||||| |||||||||||||||     | | |||   | | |     |||   ||| |||    |||   | ||| || || |      |  ||   | |||  ||||||||  |    
AAAAGATGTTCATCTGGAACCAGTGGCGTTCGACATGGAACGAGACCTTCTTACTCCAACCTACAAAAAGAAGAGGCCTCAATTGCTCAAATACTATCAGgtaa----ttttaaacattttaggcgatattatgctt-ata----atattttcggttttaaact------ctctttctattgg--tgttatttaacag--

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: AT4G23850.1 (Arabidopsis thaliana), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
 || ||  |||| |||||| || | ||||||||||||||||| || ||| | || || || | ||| ||||| ||||| |||||||| |||||||| ||||||  |     ||||  || |    ||| | |     ||| | |||    |  |   || ||||   |||     ||         || || | ||    
CAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTCAGTTGCTGAAATACTACCAGgtaata-----caaacacttt----tgcgtattgaaacatttagaaatctactgacatt-aagtat-taattaacatggtctcttcgtcatctgccag--

upper sequence: GLYMA01G43470.4 (Glycine max), 5'ss of exon 18
lower sequence: Vv02s0025g01410.t01 (Vitis vinifera), 5'ss of exon 18
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgta------caagttgtcaaattc-tctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc
 |||||||||||||||||| |  | |||||||| |||||||||||||| |||||||||||||| |||||||||||||| |||||||| ||||| |||||||||      |   |  ||| |||| |      ||     |   | | | |  || |||||  | |        | ||   | ||  ||| ||  |  | |       
CAAAGCAGTTCACCTTGACCCTGTGCCATTTGATATGGAACGTGACCTGATCACTCCAACATATAAGAAGAAGAGGCCCCAGTTGCTAAAATATTATCAGgtagctcctctgatcctcatattcatgcatgatgtgaacctgctaacaatttatggaataa-tttaagcaaaaagaattatcattgatgaaacctggtctt------

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|193669681|gb|FK607759.1|FK607759
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCCTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|254347181|gb|GR856851.1|GR856851
EST:     TCACTCCAACATACA-GA-GA-GAGGCCACAGTTGCTTAAATACTATCAG                         GATGCCATTGACA
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACA
EST: gi|193424751|gb|FK392042.1|FK392042
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|58025423|gb|CX712164.1|CX712164
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|208067869|gb|GD866181.1|GD866181
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|209712294|gb|BW668488.1|BW668488
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|208317694|gb|GE116265.1|GE116265
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|11275038|gb|BF325362.1|BF325362
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCC
EST: gi|151396024|gb|EV265901.1|EV265901
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|213605729|gb|DB976168.1|DB976168
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|213606140|gb|DB982441.1|DB982441
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|209713724|gb|BW681864.1|BW681864
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|254347182|gb|GR856852.1|GR856852
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|51342594|gb|CO983564.1|CO983564
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCTTGAGAN
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|19270925|gb|BM887181.1|BM887181
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
EST: gi|15661796|gb|BI699167.1|BI699167
EST:     TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAG                         AATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC
genomic: TCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttg ... ttgtgcacagAATGCCATTGACAACATGTATAAGAGTGGAAGTAAACCCAGTGCCTGAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGCAGTTCACCTTGACTCAATTCCATTTGACATGGAACGTGACCTTATCACTCCAACATACAAGAAGAAGAGGCCACAGTTGCTTAAATACTATCAGgtacaagttgtcaaattctctggattgcatttcacttcatattgaatagaataggtcttgaagtggataacctttataaatggaatgttatttcccctcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG