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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacatttatgttttgtgtattccatgcctttttttttttttaatttggttttggagttttcacctgattggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG

Basic information

species Glycine max
transcript GLYMA20G19000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G19000.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G356938_T01 (Zea mays), 3'ss of exon 1
--tacatttatgttttgtgta--ttccatgcctttttttttttttaatttggttttggagttttcacctgattggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
   ||  ||      ||  ||  ||  |      |        | |   ||    || |||||| |    |   ||  |  ||    |||   |  |  |||||||||||||||||||| | || || |||| || ||||||||  ||  | ||||||||||||||||| || || ||||| || ||||| |||||||  ||||
aacactatttgcccatgaatagttttaaaaaaagtcaaacagatcaccctgtgcatgtagtttttatt--acaagaactaatagcacactgctt--ttctgcagGTTGAGTCTGAGTTTTTGCCACTTTACAGCACCTATGGCATCGGATTGACTACATGGAGTCCTCTAGCTTCAGGAGTACTAACTGGAAAATATACCAAAG

upper sequence: GLYMA20G19000.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G04690.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------tacatttatgttttgtgta-ttccatgccttttttttttttt----aatttggttttggagttttcacctgat-tggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
              |   ||| | |||  | || || ||||  |   | || | ||    | | |    |||  ||  || | || | || |  |    ||   ||      |  || |||||||| | |||||||||||||||||||||||| |||| | ||| |||||||| ||||| || ||||| ||||| ||||||||||| ||||| || || |
gtttgtaatctgactctctttttctttaatttactttcatgtttgcgtcttatcttgtacagtcttaagttgttgtagtctcgtgttatgtagctcaagttatgctcttctgttatgtagGTTGAGACAGAGTTTCTTCCTCTGTACACCAACCATGGTATAGGTCTCACTACCTGGAGCCCACTTGCATCTGGTGTGCTCACTGGTAAATACAACAAGG

upper sequence: GLYMA20G19000.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0051g00650.t01 (Vitis vinifera), 3'ss of exon 1
tacatttatgttttgtgtattccatgcctttttttttttttaatttggttttggagttttca---cctg---attggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
      ||||  |        | |      ||| || ||| |  | || | |  | | || |   |||    ||  |  || | |  |   |  |||      ||||| |||| |||||  |||||||| |||| ||||||||||| ||| || || ||||||||||| ||||| || |||||||| ||||| ||||| || || |
------tatggctgacaagaactacattgatttgttgtttcatataggatgtataatgttaaaatcctttacatacggtttctgacatttttctatataaactcagGTCGAGTGTGAGTACCTTCCTCTATACAGCAACTATGGCATAGGTCTTACCACATGGAGTCCACTTGCATCAGGAGTGCTTACTGGAAAATACAACAAGG

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|19053973|gb|BM732640.1|BM732640
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|37995790|gb|CF807379.1|CF807379
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACC
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCAC-
EST: gi|192316315|gb|FK011674.1|FK011674
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|192302761|gb|FG993781.1|FG993781
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|7924550|gb|AW830576.1|AW830576
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|23731385|gb|BU763810.1|BU763810
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|10234663|gb|BE803551.1|BE803551
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAT                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|9819631|gb|BE555144.1|BE555144
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|26057670|gb|CA800584.1|CA800584
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|10844260|gb|BF067570.1|BF067570
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|6727056|gb|AW311410.1|AW311410
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|26048175|gb|CA784741.1|CA784741
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
EST: gi|20812207|gb|BQ296685.1|BQ296685
EST:     TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAG                         GTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT
genomic: TTGGTCCTATTGTTGAACAGCCTGAGTATAACCTCTTGTCCAGGCACAAGgtttttgctt ... aatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttttggagttttcacctgattggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG
                            tttttatttgactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacatttatgttttgtgtattccatgcctttttttttttttaatttggttttggagttttcacctgattggactttttatttgacttgataatgttgcagGTTGAGTCTGAGTTTCTTCCTCTGTACACCAACTATGGCACAGGCCTCACTACATGGAGTCCTCTTGCCTCTGGAGTGCTCACTGGGAAATATAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - tgttttg
- - - - - - - -tgtattc
- - - - - - - - - - - catgcct
- - - - - - - - - - - - - - - - - - - - - - - ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacctga