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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataatttttttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT

Basic information

species Glycine max
transcript GLYMA04G41090.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G067638_T01 (Zea mays), 3'ss of exon 2
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataatttt-tttcagtgtcta--atggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
       ||   || ||   || |    | |   | || || |      | |  || | |||  |||  ||    |  |   ||     |   |  |   |||| || ||||||||||| ||||| || |||||||| ||||||||  | || |||||||||||||| ||||| || |||||||| || ||| | || ||  | 
-------gtgcgttgcgccctcctccgccttgggggtgaattcagtcgatttcgttctgttttggtggatacggcgacgaggctgatggattttccgtggtcagGGGGCGGAAGAGGGCGTGTGTCACGTACTGCATCACCTACATCCTCAGCTGCATCACCAAGCACTCTCCCCAGTACAAAGTTCTTATGATTGGGCGTGTC

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataatttttttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
           |   |  | ||| || |  | ||     |||         ||| | ||||       ||||| ||| |  || |    ||||   ||||| || || |||||||| ||||| || || || || ||||| || ||||| |||||||||||||||||||||||||| || ||  ||||| | |||||  | 
----------gtgagcattctctcgtatgcttttaagtaatatggaaatcttaactcttttag-----taatgttgcataatggt-gttctgt---atcagGGGTCGTAAGAGGGCATGTGTTACCTATTGTATTACCTATATATTGAGCTGCATCACCAAGCATTCTCCTCAATATAAGGTTTTGATGGTAGGCCGTGTC

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0098g01290.t01 (Vitis vinifera), 3'ss of exon 2
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataatttttttcagtgtctaatggtgcttcttg-----cttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
             |  | |||| |  |  || ||||||   | |  | ||    |    ||      ||| |  || |||         | |  |  ||||  ||| || |||||||| |||||||||||||| ||||| || || ||  |||| ||||| ||||||||||| ||||| |||| | |  | ||| |||| ||  | 
------------gtgagatttcctactaaatgttgttgtggatccattgttctttagaattggaatcctagttttgattcacaatgccttcattcaatgaatgcagGGGACGGAAGAGAGCTTGTGTGACTTATTGCATTACTTATATACTGAGCTGCATTACCAAGCATTCACCTCAGTACAGAATTTTAATGGTGGGGCGTGTG

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 2
gtgagacgtctttttcggtttcttgtttcatcttgtt-gcatacctgtc-gtataatttttttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
             |  | |||| | ||| || ||||| |  | || |||  ||| | ||  | || ||  | ||| |  ||  | |  |||     || | || || ||||||||||| || || |||||||||||||| || ||  |||| ||||||||||||||||||||||| |||||| |  | |||||||| || || 
------------gtaagatttcct-tttgattttgtttgtttgccagtctatattaattgatccattgattcatgatattttctac--acc----aaatttagGGGTCGGAAGAGGGCATGCGTTACTTACTGCATAACTTATATACTGAGCTGCATCACCAAGCATTCTCCTCAGTACAAAATTTTAATGTTGGGACGTATA

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ11977 (Selaginella moellendorffii), 3'ss of exon 2
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataattttt--ttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
                                                |||   || ||  ||  |  |  ||| |   |||  |||    || ||    ||| ||||||||| | ||| |  | || |||||||| |||||||||||||| ||| ||||||| || |||||||| | | |||| || ||| ||||  | |||
------------------------------------------------gtaagcttcttggtttggattagaattggaattcacgctgtttctatgcg--cagTGGCCGGAAGCGAGCTAGCATAACGTACTGCATCACCTACATTTTGAGCTGCTTCACCAAACACTCTCCTCAGTTCCAAGTTCTCATGGTGGGAAGAATT

upper sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ21113 (Selaginella moellendorffii), 3'ss of exon 2
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataattttt--ttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
                                                |||   || ||  ||  |  |  ||| |   |||  |||    || ||    ||| ||||||||| | ||| |  | || |||||||| |||||||||||||| ||| ||||||| || |||||||| | | |||| || ||| ||||  | |||
------------------------------------------------gtaagcttcttggtttggattagaattggaattcacgctctttctatgcg--cagTGGCCGGAAGCGAGCTAGCATAACGTACTGCATCACCTACATTTTGAGCTGCTTCACCAAACACTCTCCTCAGTTCCAAGTTCTCATGGTGGGAAGAATT

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|208285773|gb|GE087371.1|GE087371
EST:     GGATCTTCCATGCTCCTTGGAACAATTGTCGGATCTCTAGCTGACAAACA                         AGGCCGGAAGAGGGCTTGTGTGAACTTAACTGCATAACCTACATTTTGAGT
genomic: GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACAgtgagacgtc ... gtgaaatcagAGGCCGGAAGAGGGCTTGTGTGA-CTTA-CTGCATAACCTACATTTTGAGT
EST: gi|6718954|gb|AW306601.1|AW306601
EST:     GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACA                         AGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
genomic: GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACAgtgagacgtc ... gtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
EST: gi|208215876|gb|GE015602.1|GE015602
EST:     GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACA                         AGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
genomic: GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACAgtgagacgtc ... gtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
EST: gi|193489163|gb|FK454046.1|FK454046
EST:     GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACA                         AGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
genomic: GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACAgtgagacgtc ... gtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
EST: gi|193717480|gb|FK650316.1|FK650316
EST:     GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACA                         AGGCCGGAAGAGGGCTTTGTGTGACTTACTGCATAACCTACATTTTGAGTT
genomic: GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACAgtgagacgtc ... gtgaaatcagAGGCCGGAAGAGGGC-TTGTGTGACTTACTGCATAACCTACATTTTGAGTT
EST: gi|19345775|gb|BM890655.1|BM890655
EST:     GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACA                         AGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG
genomic: GGATCTTCCATGCTCTTTGGAACAATTGTCGGATCTCTAGCTGACAAACAgtgagacgtc ... gtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgtataatttttttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT
                                   tgcttac  putative branch site (score: 2)
     taatttttttcagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagacgtctttttcggtttcttgtttcatcttgttgcatacctgtcgtataatttttttcagtgtctaatggtgcttcttgcttaccctgtgaaatcagAGGCCGGAAGAGGGCTTGTGTGACTTACTGCATAACCTACATTTTGAGTTGCATCACCAAGCATTCTCCTCAATACAAAGTCCTGATGTTGGGCCGCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC