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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgttatagttgcagtttttttgtaattggtattctgaatttctgattgaaatgattaaaacatcctgaaggcttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA

Basic information

species Glycine max
transcript GLYMA08G09570.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G02620.1 (Arabidopsis thaliana), 3'ss of exon 2
ctgttatagttg--cagtttttttgtaattggtattctgaatttctgattgaaatga---ttaaaacatcctgaaggc---ttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA
      || |||  || |  |     |||||   ||  ||| |     |||| || |   || |   ||| | || ||   ||||||    ||  || || |  |||||| ||||| ||||||||| || |||||||||| || |||||||||||| | |||||||||||||||||||| ||||||||||
----cttaattggccaatggtggcagaattg---tttggaactatccgttgatataaccctttagcaatcttcaatgccacttacaagacttaaatt-ttgtgtacagGACACTGTTGTTGGATTTTTGATGGCTGGAGTTGGTAATGTTGACATAAGGAGGAAGACAAATTACCTCATCGTGGATTCAA

upper sequence: GLYMA08G09570.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0062g00210.t01 (Vitis vinifera), 3'ss of exon 2
ctgttata-gttgcagtttttttgtaattggtattctgaatttctgattgaaatgattaaaac---atcctgaaggcttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA
    | |   |   | || |||  |  ||| ||   ||  |  |  |   | ||| ||   ||    |  |  |    |   ||| ||  ||  |  ||  ||||| ||| ||  ||| ||| || ||||||||||||| ||||||||| | || || ||||||||||| |||||||| || ||||
--actgtgcatcataattatttatttcttgataaattg--tcacaaagccacatggttttcactaggttttttatttatctgatggatgattgttcatatgcagGACACTATAACTGGGTTTTTGCTGGCTGGAGTGGGTAATGTTGACTTGCGGAGAAAGACAAATTATCTCATTGTTGACTCAA
















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|192319436|gb|FK005876.1|FK005876
EST:     ATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: ATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|209720495|gb|BW674678.1|BW674678
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGG
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACG-
EST: gi|254338552|gb|GR845695.1|GR845695
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|9984254|gb|BE658362.1|BE658362
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|31470010|gb|CD412038.1|CD412038
EST:     TATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|21887354|gb|BQ740567.1|BQ740567
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|58016543|gb|CX703285.1|CX703285
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCATATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|298198565|gb|HO040104.1|HO040104
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGCTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|6952212|gb|AW424280.1|AW424280
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|192294996|gb|FG986715.1|FG986715
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|213604582|gb|DB966669.1|DB966669
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|8284082|gb|BE021641.1|BE021641
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|193347072|gb|FK311404.1|FK311404
EST:     CTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: CTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|298165832|gb|HO008803.1|HO008803
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|13311850|gb|BG405501.1|BG405501
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGATTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|298182781|gb|HO031516.1|HO031516
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|15813300|gb|BI785575.1|BI785575
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|6724545|gb|AW308944.1|AW308944
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|193688464|gb|FK634455.1|FK634455
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGG
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGG
EST: gi|13252581|gb|BG363484.1|BG363484
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|254338553|gb|GR845696.1|GR845696
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|12497052|gb|BG047373.1|BG047373
EST:     TC-AATTCCTACC-ACAATTCAGCCCTTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTTGGCTGGAGTGGNAAATGTTGACATACG
genomic: TCAAATTCCTACCAACAATTCAGCCC-TCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTG-TTGGCTGGAGTGGGAAATGTTGACATACG
EST: gi|213594238|gb|DB966139.1|DB966139
EST:     TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: TTCAAATTCCTACCAACAATTCAGCCCTCATTGCTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
EST: gi|193413995|gb|FK376589.1|FK376589
EST:     CTATGATTGCAGATGAG                         GATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT
genomic: CTATGATTGCAGATGAGgtaagagtgt ... ttttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgaaatgattaaaacatcctgaaggcttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA
                         ggcttac  putative branch site (score: 3)
                                        ctttatttt  putative PPT
                            ttacaatgaatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgttatagttgcagtttttttgtaattggtattctgaatttctgattgaaatgattaaaacatcctgaaggcttacaatgaatactttattttacacagGATACTGTAGTTGGATTTCTGTTGGCTGGAGTGGGAAATGTTGACATACGTAGGAAGACAAATTACCTCATTGTGGATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - gttgcag
- - - - - - - - - - - - - - - - - - - - - ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgaa