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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcaaactttcactttcactttgtgtgtgcgcttttcatgatattttgtggaatttgaagccaataaatacagacatatatatagtgttgacattttgaatagtataattgggtgtcggtattcaaagattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 4
---------gtatgtcaaactttcactttcactttgtgtgtgcgcttttcatgatattttgtggaatttgaagccaataaatacagacatatatat------agtgttgacattttgaatagtataattgggtgtcggtattcaa----agattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG
           || | ||  |     |    ||||   | |  | | ||  | || |||  |||   |||    || | |  |    ||||| |||      |||       ||     |  |  | ||    ||  ||| | ||    | |  ||| | | ||  ||||  ||| ||||| || |||||||||||| |  | || || || ||||| ||||||||||||||||||||||| || ||||||||||
gtaagaagaagatattaatttccttatcatgcttttcttttatggtatttgtaatgtttactggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttccttcttttggatttcctggttagtactgaagtagaaagagtgaaacctt--ttatc-ttttagGTACATGGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 4
---------gtatgtcaaactttcactttcactttgtgtgtgcgcttttcatgatattttgtggaatttgaagccaataaatacagacatatatat------agtgttgacattttgaatagtataattgggtgtcggtattcaa----agattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG
           || | ||  |     |    ||||   | |  | | ||  | || |||  |||   |||    || | |  |    ||||| |||      |||       ||     |  |  | ||    ||  ||| | ||    | |  ||| | | ||  ||||  ||||||||| ||||||||||||||| |  | || || || ||||| ||||||||||||||||||||||| || ||||||||||
gtaagaagaagatattaatttccttatcatgcttttcttttatggtatttgtaatgtttactggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttccttcttttggatttcctggttagtactgaagtagaaagagtgaaacctt--ttatc-tttcagGTACATTGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0211g00160.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------gtatgtcaaactttcactttcactttgtgtgtgcgcttttcatgatattttgtggaatttgaagccaataaatacagacatatatatagtgttgacattttgaatagtataattgggt------gtcggtattcaa----agattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG
                                   |  ||   | ||  | | |   || ||    | | | ||  | || | |  |||   |||    || | |  |    ||||| |||   ||            |  |    |||| |      ||  ||| | ||    | |  ||| | | ||  ||||  ||||||||| ||||||||||||||| |  | || || || ||||| ||||||||||||||||||||||| || ||||||||||
gtaagaagatattaatttccttatcatgattttctttcgtggtatttgtaatgtttattggtcatcgtggtatttgtaatgtctattggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttcattcttttggatttcctggttagtactgaagtagaaagagtgaaacctt--ttatc-tttcagGTACATTGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------gtatgtcaaactttcactttcactttgtgtgtgcgcttttcatgatattttgtggaatttgaagccaataaatacagacatatatatagtgttgacattttgaatagtataattgggt------gtcggtattcaa----agattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG
                                   |  ||   | ||  | | |   || ||    | | | ||  | || |||  |||   |||    || | |  |    ||||| |||   ||            |  |    |||| |      ||  ||| | ||    | |  ||| | | ||  ||||  ||||||||| ||||||||||||||| |  | || || || ||||| ||||||||||||||||||||||| || ||||||||||
gtaagaagatattaatttccttatcatgattttctttcgtggtatttgtaatgtttattggtcatcgtggtatttgtaatgtttattggtcattgttatcatttagcattatcatatttatgtagtcagttccagtgttcattcttttggatttcctggttagtactgaagtagaaagagtgaaacctt--ttatc-tttcagGTACATTGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAG

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|193445566|gb|FK412657.1|FK412657
EST:     GGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: GGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|208263551|gb|GE063811.1|GE063811
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193438324|gb|FK400033.1|FK400033
EST:     CCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: CCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|207839851|gb|GD810044.1|GD810044
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193392902|gb|FK359678.1|FK359678
EST:     AATGAAGGATATTCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AATGAAGGATA-TCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193712073|gb|FK648816.1|FK648816
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|208217137|gb|GE008617.1|GE008617
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193469321|gb|FK437627.1|FK437627
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193588700|gb|FK540098.1|FK540098
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|207765710|gb|GD735955.1|GD735955
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193408671|gb|FK374173.1|FK374173
EST:     AATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|208083475|gb|GD883985.1|GD883985
EST:     GGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: GGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193367587|gb|FK332049.1|FK332049
EST:     AATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAAACGTGCCTTGGAAGCAT
genomic: AATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTC-AAAAACGTGCCTTGGAAGCAT
EST: gi|207789742|gb|GD763456.1|GD763456
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATGTTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|208025377|gb|GD823425.1|GD823425
EST:     CCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: CCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|207779220|gb|GD750750.1|GD750750
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193515317|gb|FK472879.1|FK472879
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAG
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAG
EST: gi|193595490|gb|FK554355.1|FK554355
EST:     AACACTCGGAACGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTAAAGCCTTGGAAGC
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGT---GCCTTGGAAGC
EST: gi|208209401|gb|GE003853.1|GE003853
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193471231|gb|FK438124.1|FK438124
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATCGTCAAAA-CGTGCCTTG
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTAT-GTCAAAAACGTGCCTTG
EST: gi|193633479|gb|FK579649.1|FK579649
EST:     AAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATCGTC-AAAACGTGCCTTGGAAGCAT
genomic: AAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTAT-GTCAAAAACGTGCCTTGGAAGCAT
EST: gi|208310329|gb|GE105549.1|GE105549
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATG
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATG
EST: gi|193308001|gb|FK272023.1|FK272023
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
EST: gi|193628730|gb|FK574570.1|FK574570
EST:     AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGA                         GTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT
genomic: AACACTCGGAATGAAGGATATCCCGGTGCAAGATATTATGGGGGAAATGAgtatgtcaaa ... attatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtataattgggtgtcggtattcaaagattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG
                                              ttatttc  CT-rich tract
                                   atctttatttattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcaaactttcactttcactttgtgtgtgcgcttttcatgatattttgtggaatttgaagccaataaatacagacatatatatagtgttgacattttgaatagtataattgggtgtcggtattcaaagattgtggatctttatttattatttcagGTATATTGACATGGCAGAAACACTATGTCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG