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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagtctaatgaagaggttgtgtgtgttataatggaagtagtctaaatgttatgtattttgataaagaaatttgttgatgttaaaatgttgtttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCAAATGCCGAAAACGCGTATTACAAGTCCATGGGAACTGATACATCTAATT

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 14
--aagtctaatgaagaggttgtgtgtgttataatggaagtagtctaaatgttatgtattttgataaagaaatttgttgatgttaaaatgttgtttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCAAATGCCGAAAACGCGTATTACAAGTCCATGGGAACTGATACATCTAATT
  || | || |    |  ||| || | |  |  |    ||| |  |    ||    |||   ||||     |  |      ||      || || || | ||||||||||| |||||| ||| |||||||||||||| |    |||  || | ||||||||||| || |||||||||   ||||||| | || |  | ||||
ttaaatttatttttta--ttgggtttatagttgttattgtattgcattaattggtgattccaataattgtttacgggatatttctgtctttattggttccagGTGAGGGAGAGGTGTAAAAAAGAGTGGACCATGTTTCGAGTTCGCATGACCAATGCCGAAAAAGCATATTACAAGGAGATGGGAATTAATCCTACCAATT

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv17s0000g02780.t01 (Vitis vinifera), 3'ss of exon 2
--aagtctaatgaagaggttgtgtgtgttataatggaagtagtctaaatgttatgtattttgataaagaaatttgttgatgttaaaatgttgtttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCAAATGCCGAAAACGCGTATTACAAGTCCATGGGAACTGATACATCTAATT
  || | || |    |  ||| || | |  |  |    ||| |  |    ||    |||   ||||     |  |      ||      || || || | ||||||||||| |||||| ||| |||||||||||||| |    |||  || | |||||||||||  | |||||||||   ||||||| | || |  | ||||
taaaatttatttttta--ttgggtttatagtttttattgtattgcattaattggtgattccaataattgtttacgggatatttctgtctttattggttccagGTGAGGGAGAGGTGTAAAAAAGAGTGGACCATGTTTCGAGTTCGCATGACCAATGCCGAAAAAACATATTACAAGGAGATGGGAATTAATCCTACCAATT

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv14s0036g00790.t01 (Vitis vinifera), 3'ss of exon 2
--aagtctaatgaagaggttgtgtgtgttataatggaagtagtctaaatgttatgtattttgataaagaaatttgttgatgttaaaatgttgtttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCAAATGCCGAAAACGCGTATTACAAGTCCATGGGAACTGATACATCTAATT
  || | || |    |  ||| || | |  |  |    ||| |  |    ||    |||   ||||     |  |      ||      || || || | ||||||||||| |||||| ||| |||||||||||||| |    |||  || | |||||| |||| || |||||||||   ||||||| | || |  | ||||
taaaatttatttttta--ttgggtttatagttgttattgtattgcattaattggtgattccaataattgtttacgggatatttctgtctttattggttccagGTGAGGGAGAGGTGTAAAAAAGAGTGGACCATGTTTCGAGTTCGCATGACCAATGCCAAAAAAGCATATTACAAGGATATGGGAATTAATCCTACCAATT

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|6726342|gb|AW310696.1|AW310696
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
EST: gi|19348792|gb|BM893324.1|BM893324
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
EST: gi|192319062|gb|FK010626.1|FK010626
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
EST: gi|208125922|gb|GD925978.1|GD925978
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
EST: gi|254315636|gb|GR825445.1|GR825445
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
EST: gi|254347136|gb|GR856806.1|GR856806
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA
EST: gi|193385504|gb|FK349858.1|FK349858
EST:     GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGG                         -TGAGGGAGCGGTGTAGAAAGGAGTGGACCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCA
EST: gi|192302164|gb|FG995816.1|FG995816
EST:     GGTGAATTTCAAACAGGGAAATCACGGTGGCAGGGG                         GTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGGGTCGGTTGGCA
genomic: GGTGAATCTCAAACAGGGAAATCACGGTGGCAGGGGgtatgttact ... tttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttatgtattttgataaagaaatttgttgatgttaaaatgttgtttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCAAATGCCGAAAACGCGTATTACAAGTCCATGGGAACTGATACATCTAATT
                          tgttgat  putative branch site (score: 4)
     atgtattttgataaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagtctaatgaagaggttgtgtgtgttataatggaagtagtctaaatgttatgtattttgataaagaaatttgttgatgttaaaatgttgtttgtgctagGTGAGGGAGCGGTGTAGAAAGGAGTGGACCATGTTCCAGAGTCGGTTGGCAAATGCCGAAAACGCGTATTACAAGTCCATGGGAACTGATACATCTAATT

- - - aatgaag
- - - - - - - ggttgtg
- - - - - - - - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttgatg