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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc...

Basic information

species Glycine max
transcript GLYMA04G37030.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 5'ss of exon 3
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttgcaacct---tgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc
  |||||| ||||||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||| || |||||||| |||||  | || || ||||| |  ||| |||| |   ||  ||| || |    ||| |  |           |  |||||  ||   ||||                              
AACTGTGAGGAAAATTATTGAAATAAATCCGTACATGCTTGGAACAATGGCAGGAGGTGCTGCTGATTGTCAATTTTGGCATAGGAACTTGGGCATCAAGgttagattt-caacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttt--tcag------------------------------

upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G102596_T02 (Zea mays), 5'ss of exon 3
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgt--aatctttgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc
  | |||| ||||||||| ||||| ||||| || ||||| |||||||||||||| ||||||||||||||||| |||||||| ||||| || || |  |||||   |  |  ||  ||||    | |  ||||   ||| ||||   |   ||    ||     | |  |  ||    | | |                    
AACCGTGAGGAAAATTATTGAAATAAATCCTTACATGCTGGGGACAATGGCTGGAGGTGCTGCTGATTGCCAATTTTGGCATAGGAACCTAGGAACCAAGgtcagaagtcggcttcctttcaataattatctcttatg-ttgcccct--ttgcagggtggggctaacataggttcttttcag--------------------

upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: AT1G13060.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatc--tttgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc
 ||||||||||| ||||| ||||||||||| |||||||| || ||||||||||| || |||||||||||||| || |||||||| ||||| || |||||||||      | | || |||          |||    || |  |||    || ||   | ||||||   || ||      | | | |  |||     | |   
ATCTGTGAAGAAGATTATTGAAATCAATCCTTATATGCTCGGTACAATGGCTGGAGGAGCTGCTGATTGCCAATTCTGGCACAGAAATCTTGGAATTAAGgtacctaactagaaatctttttggccgtgtctgaactgataacttggatct-ttgattaatctttctctctgtggttatcgggaatcttgctgccttgtta-

upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctt-tgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc-
 ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| || || |||||||| ||||| || |||||||||  ||   |  |  ||  | |  |  |  || || | || ||  | || | | ||||||||     | ||  |   |||  |   |   |   || |   
ATCTGTGAAGAAGATTATTGAAATTAATCCTTATATGCTTGGTACAATGGCTGGTGGTGCTGCTGATTGTCAATTCTGGCACAGAAATCTGGGAATTAAGgtaccctaacgttagtttttgttagct-ttctgaattgatgattgggtctat-cagttatcttccttgctgtggcaatccggttacttcttaccttcccttt

upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 5'ss of exon 4
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttgcaaccttgagcttacaatcttgcatggttgcttttgcctgt--tctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc
 ||||||||||||||||| ||||| ||||| || |||||||| ||||||||||| || |||||||||||||||||||||||||| ||| | || ||||||||||| | |      |||   |  | |  |||||   ||  |   ||||||  |||   ||  ||| |  |   |      | | || | |           
ATCTGTGAAGAAAATTATTGAAATTAATCCCTACATGCTTGGCACAATGGCTGGAGGAGCTGCTGATTGCCAGTTTTGGCACAGAAATTTGGGCATTAAGgtaatgtatttt-tgttgttttctctaatttgcactctttttcaggcctgtgatctacaataattatggaatgatttgatagtactggttctgctactgta-

upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: PP1S2_300V6.1 (Physcomitrella patens), 5'ss of exon 3
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgta---------atctttgcaaccttgagcttac--aatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc
 || |||||||||||| | |||||||| || ||  || | || ||||||||||| |||||||| ||||| |||||||||||  | ||||| || |     |||         |  ||||   | |  || |  |  ||| | | |  || |  | ||  | |   |  || || | |  ||||  || | |   |    || ||       
ATCGGTGAAGAAAATTTTGGAAATCAACCCTTACTTGTTGGGCACAATGGCTGGAGGTGCTGCAGATTGTCAGTTTTGGCAACGAAATCTAGGCACACGAgtatctcaacgtacttttgttgcttctagttctctgaatgtagaacagtaggctgtgagtatgtgg--atgttcatgcaagtcaactactgggat--cacagta-------

upper sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 4
lower sequence: EFJ25863 (Selaginella moellendorffii), 5'ss of exon 3
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc
||| |||||||||||| | ||||||||||| ||| | || || || |||||||| ||||| || ||||| ||||| ||||| || |||||||| |    |||||  ||      |||          || | || | ||        ||||||  ||   |    |                                  
GTCGGTGAAGAAAATTCTGGAAATCAATCCATATCTCCTGGGAACCATGGCTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagttt----gtcttcgctccttcttcctccacgattttgacactctgttcgtttgaatcacag----------------------------------

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|254321270|gb|GR824587.1|GR824587
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|58021915|gb|CX708656.1|CX708656
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTGGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|193462440|gb|FK425525.1|FK425525
EST:     CTGGAGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|6227844|gb|AW156443.1|AW156443
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAANTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|254338527|gb|GR849945.1|GR849945
EST:     CTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|192322800|gb|FK014491.1|FK014491
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|254322198|gb|GR837612.1|GR837612
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|8827593|gb|BE211323.1|BE211323
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|192319717|gb|FK013759.1|FK013759
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|151410487|gb|EV280302.1|EV280302
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCGTGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|15814359|gb|BI786634.1|BI786634
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|193584124|gb|FK541504.1|FK541504
EST:     CTGGAGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|192319718|gb|FK013760.1|FK013760
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|298189385|gb|HO037788.1|HO037788
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
EST: gi|58014664|gb|CX701406.1|CX701406
EST:     CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAG                         TGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC
genomic: CTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttg ... attattttagTGTCGTTTGCATGAGTTGGCAAATAAAAGGAGAATTTCAGTGACAGGAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGTGAAGAAAATTATCGAAATCAATCCGTATATGCTTGGGACAATGGCTGGTGGTGCTGCTGATTGCCAGTTTTGGCACAGGAATCTCGGGATTAAGgtaatctttgcaaccttgagcttacaatcttgcatggttgcttttgcctgttctgttatctttaggtcagtctcctgccgaattgctgcaatagtctccc

- - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT