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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttcaaaaatcagatgacctcaatttttttttcatgctgatataaaatttaaattcaattgtttgcaacttttttctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT

Basic information

species Glycine max
transcript GLYMA20G33630.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G04850.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttcaaaaatcagatgacctcaatttttttttcatgctgatataaaatttaaattcaattgtttgcaacttttttctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT
             |  |   |  || |||||| | ||  |  ||  |||    |   || |       |||     || | |       |   | |  ||||||||||  | || ||||| ||||||||| |||| |||||||||||||| || ||||| ||||| || |||
-----------gtatgtactcataagttttttcttatcttcttagtaaaaaatagcacattgaaccaaaac----ctcatgtacatgaatgaatatgcagATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGAT

upper sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 3'ss of exon 3
gttttcaaaaatcagatgacctcaatttttttttcatgctgatataaaatttaaattcaattgtttgcaacttttttctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT
                 |     | || || ||   | ||  | ||| |  |   |||||| ||||| |   || |   | | ||   |   ||    ||||||||||  | || ||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||||
-----------------gtatgtatttcttgttctcttctcttctaagaggtg--ttcaat-gtttgaatggttgtgtatctattaaatctgctgc--agATGACAGCACTAAAATCTGCGAACAAGGAGTTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATTGAT

upper sequence: GLYMA20G33630.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 3'ss of exon 3
-gttttcaaaaatcagatgacctcaatttttttttcatgctgatataaaatttaaattcaattgtttgcaactttttt----ctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT
  | || ||        | |   ||| |   |||| ||     | |    |||  ||||  |||  || |  || |||    ||  || |       ||||| ||||||||||||||||  |||| ||||||||||| || ||||||||||| |||||||||||  |||| || |||
aatgtttaatctcttttttattccaaatgcatttttat-----tttgcggttttcattcgtttggctgaagtttctttgaatctaattattatgcttcttttcagATGACAGCTTTGAAAGCTGCAAACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGAT

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|298174856|gb|HO014773.1|HO014773
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGCTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|254325618|gb|GR838499.1|GR838499
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|298171425|gb|HO016457.1|HO016457
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|298163684|gb|HO012417.1|HO012417
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|192326636|gb|FK018853.1|FK018853
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|151397618|gb|EV267491.1|EV267491
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|58024021|gb|CX710762.1|CX710762
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|298199136|gb|HO042499.1|HO042499
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|298176762|gb|HO023235.1|HO023235
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|254325619|gb|GR838500.1|GR838500
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|192314082|gb|FK010362.1|FK010362
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
EST: gi|192294647|gb|FG986496.1|FG986496
EST:     TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACT                         ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT
genomic: TCGATCAAGTTCAATTTGCTGCTGAGGGCATTAAAGATGCTCAACAAACTgtatgtatca ... ccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatttaaattcaattgtttgcaacttttttctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT
               ttgtttgcaacttttt  CT-rich tract
                       aacttttttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttcaaaaatcagatgacctcaatttttttttcatgctgatataaaatttaaattcaattgtttgcaacttttttctttttttcccttccctttttagATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - tgacctc
- - - - - - - - - - - - - - - - -tcatgct