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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG

Basic information

species Glycine max
transcript GLYMA16G12080.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------agaatt-gtggaactaattccca-cactagttctatttttattttaatttagttctctttg--gaaatttgat---tttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
                                                                               || || || | ||     |  |  | |   |||    | | |||| || | |  | |||    | | || |    ||| |||||    | | | |     |  |||||||||| | ||||| ||||| || || ||| |||||||||| || |||||||| || ||  ||||||||||| ||||||| ||   |  |||     | 
gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G016551_T01 (Zea mays), 3'ss of exon 1
-agaattgtggaactaattcccacactagttctatttttattttaatttag-ttctctttggaaatttgattt---tgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
     || |   |  || ||| |    ||     ||   ||| |  |  |   |     | | | | |||  |   ||| |   |  | ||  || || |  ||| |||||||||||||| || ||||||||||| ||||||||||| || ||| | || |||||||| ||||| ||| |||| |||||| |    ||     | 
gtattttttaataaaaaatcctaggacagggtgtttgccattcttttgcaaactgatactagcattatgacctaactgtattgttattgtgcctatcaaa--cagATTTGCTCGTGTTGGCTCTGTTGTTTTAGCCCTTCATGATGCAAGTGATATATTCCTAGAGATTGGGAAGATGGCCAAGTACAGTAGCTGCGAGTGGCTA

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G163426_T01 (Zea mays), 3'ss of exon 3
--agaattgtggaactaattcccacactagttctatttttattttaatttag-ttctctttggaaatttgattt---tgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
  |   || |   |  | |||| |    ||    |||   ||| |  |  |   |     | | |   |||  |   ||| |   |  | ||  || || |  ||| || |||||||||||  | ||||||||||| ||||||||||| || ||| | || |||||||| ||||| ||| |||| |||||| |    ||     | 
gtatttttttaataaaatttcctaggagagggtgattgccattcttttgcaaactgatactagcatcatgacctagctgtattgttgttgtgcctatcaaa--cagATTCGCTCGTGTTGGCACTGTTGTTTTAGCCCTTCATGATGCAAGTGATATATTCCTAGAGATTGGGAAGATGGCCAAGTACAGTAGCTGCGAGTGGCTA

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
--agaattgtggaactaattcccacacta-gttctatttttattttaatttagttc-tctttggaaatttgattttgtt-tctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
  |   ||        |  ||| |  |||   |  |         | |||   ||  ||        |||||| || || | |||| |    || |    |  || ||  | |||||||| || |||||| | |||||||| |||||||| ||||||||||| ||| | ||||||||||| ||||| ||||| ||||||| ||| 
gtatgcttccatcgtcacatcctattctatactgaaaaacagaactgattccttttgtccacattgttttgatcttcttgtttctttttctctttatcgctgtagCTTCTCCCGTGTTGGTTCTGTTGTTCTGGCACTTCACGATGCTAGTGATGTGTTTCTTGAGGTTGGGAAAATGTCTAAATATAGTGGAGCTGAAAGAATC

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G25540.1 (Arabidopsis thaliana), 3'ss of exon 4
agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
                | |  | | ||  |  | || | || |     |            | | |  ||||||||   ||  ||||| |  | ||  || ||  |||||| ||| || ||| || | |||||||||||||| ||||||||||| || || || ||||||||||| |||||  | || || ||||   | 
---------------gtacgtatatta--tacacttgtgttgtggaggaaaggatacactgactcttgttttgttt---ttggatgttgatgatat--agATTAACTCGTGCTGGTTCTGTTATTCTTGCACTTCATGATGCGAGCGATGTGTTCCTTGAAATTGGGAAAATGTCTAAATATTGCGGAGCGGAAAGTCTC

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0010g01110.t01 (Vitis vinifera), 3'ss of exon 3
agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
| |||  | | | |   |   | |  |  | |  |   || ||  |||  |||| | |   |  ||  |||| |||||||   || | |  | | | ||| || || |||||||| || ||||||||||| |||||||||||||| ||||| ||||| ||| ||||||| |||||||||||||  ||||||||||| |  
aaaatgtttggatttcatagtaaataatcttttatgcaatatttctttctttctttctttcatcttttttttttttctctctgatttctgtctcttgcagATTCGCCCGTGTTGGTTCTGTTGTTTTAGCTCTTCATGATGCTAGTGATGTCTTTCTGGAGGTAGGGAAGATGTCCAAATACAAAGGTGCTGAAACCACT

upper sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_229V6.1 (Physcomitrella patens), 3'ss of exon 3
agaattgtggaactaattcccacactagttc--tatttttattttaatttagttctctttggaaatttg---attttgtttc--tcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
    ||| |||| |  |  | | | |  ||        || ||| | || ||  |     ||||||      | |  | ||     | | ||||||        ||| || |||||||||||||| || ||  | ||  | ||||||||||||||||| |||||||| |||||||| ||| | ||||| || |||   || |  || 
----ttgaggaa-tgctgacaaaagtgatttatcgacgttctttcagttgagaaccgcgaggaaatacacaaactgagctttgacgtgccatgtttggttgg--cagATTAGCTCGTGTTGGATCTGTGGTCCTGGCTGTGCATGATGCTAGCGATGTATTTCTAGAAATAGGGAAGATGACAAAATATAGCGGTCTGGAGATCATT

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|5760327|gb|AI965754.1|AI965754
EST:     AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTNTTAG                         GTTTGCTCGTCGT-GGATCAGTTGTTNTAGCACTTCATGATGCTAGCGATG
genomic: AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatcttttt ... acacattcagGTTTGCTCGT-GTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATG
EST: gi|151411962|gb|EV281773.1|EV281773
EST:     AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAG                         GTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT
genomic: AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatcttttt ... acacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT
EST: gi|151408094|gb|EV277902.1|EV277902
EST:     AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAG                         GTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT
genomic: AGTCATCATGTTGCTACTGTAATTCTTATTGTTCTGTCTTACATTTTTAGgtatcttttt ... acacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG
                                        gtttaac  putative branch site (score: 3)
               aaatttgattttgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaattgtggaactaattcccacactagttctatttttattttaatttagttctctttggaaatttgattttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATG

- - - - - - - - ttcccac