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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA

Basic information

species Glycine max
transcript GLYMA08G46090.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G349810_T01 (Zea mays), 3'ss of exon 2
-acttcccttttttcgtttgcacacttg---tccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA
 |      ||   || |||| |   |||     || | ||||| ||  |  ||||  | || ||       ||  |  |||    || |  | |   |   ||||| ||||||||  |||||||||||| |||||||||  |||| | |||||||||| ||||| | ||| | ||||  ||||| |||   |  ||  |||| |
aagaatgtttaggtcatttgtattgttgaaaagcaatctcatgttagtg--gatttatatgaca--caggactggatgaattcatatttaatcttgtcacacagGACAAGGAGTCTCGGGATTTGAACAATGAAGAGAAGATTGAGGTTGCTGGTAAGGAGAAACAGGAATGGAATGCATTGTTCAAATTGGACAAATATGCTA

upper sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 8
lower sequence: AT5G48570.1 (Arabidopsis thaliana), 3'ss of exon 8
acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA
              ||  |   | |   |  | |   || | |   |   | | |    |   |||  | |  ||||  || ||   | |||   | |||||||| ||||| |||||| |||||||  | || |   | |||||||| || ||||||||||||||||| ||||||||||| |||||||| ||  | ||||
--------------gtgagaggattca-ctttctgagtgttgtttctttctttatgaagaaacttaagtgtgctaatgata-tcgtctctcttgatgcagGAGAAAGAGTCTTGGGATATGAACACACAGGAAAGGATAGAAGCTGCAGGCAAGAAGAAAGAAGAAGGCAATGTGTTGTTCAAAGCTGGAAAATACGCAA

upper sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 8
lower sequence: AT3G25230.1 (Arabidopsis thaliana), 3'ss of exon 8
acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttc-agGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA
   |   |    |  |||| |  ||| | |    |||   |   |    | | | ||| ||| | |        ||   |  | |||  |  || ||  |||| | ||| || |||||  |||||||||| |||||  ||||||||||| |||||||||| ||||||||||||     ||||||||  || ||  || |  
--gttagtgaagtattttggatgcttatgc-cgctcacaattcag----tcaatatggaagtataagagtc--caacacttgtttgtcattggctttttagGAAAGGGAATCGTGGGACATGAACACTGAGGAGAAGATTGAAGCTGCTAGTAAGAAGAAGGAAGAAGGAAATTCCAAGTTTAAAGGAGGCAAATATTCCC

upper sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 8
----acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA
           |||||||||    | | || |   |   |||| |||  ||  |   |||   |  |   |   |        | | |||   | | | ||||||| ||||| || |||||| ||||||||||||||||  |||| |||||||| |||||||| |||||||| |||||| | || || ||||||||  ||||||
gtctgtaatatttttttcgtccaaata-ttctttttccacatgatatctatagta--tttcataactaagt---tgacgtgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA

upper sequence: GLYMA08G46090.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 3'ss of exon 4
----acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA
           || |||||| |  | | || |   |  ||||| |||  || ||   |||   |  |   |   |   |    | | |||   | | | ||||||| ||||| || |||||| ||||||||||||||||  |||| |||||||| |||||||| |||||||| |||||| | || || ||||||||  ||||||
gtctgtaatatttgtttcgtctaaata-ttctttttcctcatgatatctataata--tttcataactaagt---tgacatgtgttacctggcctattctttcagGACAAGGAATCTTGGGATATGAACACTGAAGAGAAGATTGAGGCTGCTGGCAAGAAGAAGGAAGAAGGCAATGTGCTATTCAAGGCTGGTAAATATGCAA

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|193717162|gb|FK655588.1|FK655588
EST:     CTCCTAACTCAACNGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
EST: gi|207709936|gb|GD690620.1|GD690620
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
EST: gi|193637038|gb|FK582213.1|FK582213
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGG
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGG
EST: gi|208301049|gb|GE098532.1|GE098532
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
EST: gi|208073488|gb|GD868973.1|GD868973
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
EST: gi|193566984|gb|FK525085.1|FK525085
EST:     TAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAG                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: TAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
EST: gi|208141220|gb|GD934386.1|GD934386
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
EST: gi|207778171|gb|GD748356.1|GD748356
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGG
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGG
EST: gi|193571449|gb|FK531784.1|FK531784
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGG
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGG
EST: gi|193387272|gb|FK349553.1|FK349553
EST:     CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAA                         GAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT
genomic: CTCCTAACTCAACTGTTTATTTTGAAGTTGAGCTAGTTTCATTTGAGAAAgtaagtcaat ... ctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA
                               tcttaat  putative branch site (score: 3)
                                     tctgttttctgccttc  CT-rich tract
                            taatcttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttcccttttttcgtttgcacacttgtccattttcatgctatggatgattattttggcagttttatctctagtaatcttaatctgttttctgccttcagGAGAAGGAGTCCTGGGATTTGAACACTGAAGAGAAACTTGAAGCTGCTGGTAAGAAGAAAGAAGAAGGAAATGTGTTGTTTAAAGCTGGTAAGCATGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
-cttccct
- - - - - - - - -tgcacac
- - - - - - - - - - - - - - - - - tcatgct
- - - - - - - - - - - - - - - - - - - - - tggatga