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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA

Basic information

species Glycine max
transcript GLYMA05G31030.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S422_18V6.1 (Physcomitrella patens), 3'ss of exon 3
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatg--atattattggcgtcaaaacccc-ttgaaattgatttgtgtt--ttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
    | | |   ||  ||  || |  |  ||        ||||| ||| |   |   ||| ||   | ||| |||  | |||    ||     | ||  |  |||||||||||| | ||||| || ||||| || || || ||||||||||| ||||| || || ||| | ||||||||  |||| ||||| ||||| |||||||
----actatgacatactag-tgtaggacattggcaagagttttgcatttatgagttgtataatgatcatcagaacgacgttgtccatgcccccttttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA

upper sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattg--atttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
 |  |      |||| | | || | ||| || | | ||    |   ||   | |  ||| || |||   |       |||  ||    ||| || ||  |||||||||||||| ||||| ||||||||||| || || || |||||||| |||||||| || ||  | ||||| ||  ||||||||||||||||    || |
gtacacgcaactatgttta-tgcagcagtttaaggtcctgcgtactttgtgaaggaatt-ttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA

upper sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S433_16V6.2 (Physcomitrella patens), 3'ss of exon 3
--atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
   |   || | ||     | ||    ||  | | ||           |||||     || ||  | || |      | |   |||   || | |||| |||||||||||| | ||||| || ||||| ||||| |||||||| ||||| ||||| || || ||| | ||||| ||  |||| ||||||||||| ||||| |
tagttggatatgttgcaggagctcctgcatttatgagttgtagaatagttaacg-atgatcatcagtgtgacgttgtccttttattctcttttctttt-cagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA

upper sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S3_616V6.1 (Physcomitrella patens), 3'ss of exon 3
atctaatttcttatgataactgaatcaggt-ttaagccccttttggattaaca------tgatattattggcgtcaaaaccccttgaaattgatttgtgtttt---acagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
          |     | ||||  |||||   |    | ||||||   ||  |       || |  || |  || || ||    |  | || |||  | |||     |||||||||||| | ||||| ||||||||||| || |||||||||||||| ||||| || || ||  | ||||| ||  |||| ||||||||||| ||||| |
----------tccaagtgactgtttcaggagctccatctcttttgagctagtaaagcagcgacagaatcgtagtgaacacttgattgagtttattattttttctgcgcagGTTGATTATTCCTGCACTCCAGAAGAAGTACAACAACACTTTCAGTCATGTGGCACAGTGAATCGCGTCACAATTTTGACCGACAAGTTTGGACAGCCAA

upper sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23874 (Selaginella moellendorffii), 3'ss of exon 3
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
                               |||| |   |||    |    |  | |  ||| | |  ||   | | |  | || | |||  ||   |||| |||||| | ||||||||||| ||||| || ||||||||||| |||||||| ||||| ||| |||| ||||| || ||||||||||| || ||||| |
------------------------------gtaagtcttcttt----tcttctcttctcgttgccttggaa---cttagtgagtggtatgttctt---agGTGGATTATTCGTGCACACCAGAGGAAGTCCAACAACACTTTCAATCCTGTGGCACTGTTAACCGGGTTACTATTCTAACTGACAAGTTCGGACAGCCCA

upper sequence: GLYMA05G31030.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10007 (Selaginella moellendorffii), 3'ss of exon 2
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
                               ||||     |||    |    |  | |  ||| | |  ||   | | |  | || | |||  ||   |||| |||||| | ||||||||||| ||||| || || |||||||| |||||||| ||||| ||| |||| |||||  | ||||||||||| || ||||| |
------------------------------gtaagttttcttt----tcttctcttctcgttgccttggaa---cttagtgagtggtatgttctt---agGTGGATTATTCGTGCACACCAGAGGAAGTCCAACAGCACTTTCAATCCTGTGGCACTGTTAACCGGGTTACTATTTTAACTGACAAGTTCGGACAGCCCA

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|208215175|gb|GE012372.1|GE012372
EST:     CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
EST: gi|193705269|gb|FK643093.1|FK643093
EST:     CTCAGGCAAACAAGGAGGAGGCAGATGCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
EST: gi|7686310|gb|AW756886.1|AW756886
EST:     CTCAGGCAAACAAGGAGGAGGCAGATGCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
EST: gi|192304231|gb|FG993529.1|FG993529
EST:     CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
EST: gi|208204768|gb|GE005669.1|GE005669
EST:     TCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTT
genomic: TCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTT-GTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTT
EST: gi|208292012|gb|GE090684.1|GE090684
EST:     CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAAC
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAAC
EST: gi|193578737|gb|FK538097.1|FK538097
EST:     CTCAGGCAAACAAGGAGGAGGCAGATGCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
EST: gi|192295407|gb|FG987021.1|FG987021
EST:     CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
EST: gi|208127439|gb|GD925815.1|GD925815
EST:     CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAAT                         GTTGATTATGCATGCACACCAGAAG
genomic: CTCAGGCAAACAAGGAGGAGGCAGATTCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA
      atgatattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctaatttcttatgataactgaatcaggtttaagccccttttggattaacatgatattattggcgtcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACTGACAAGTTTGGCCAGCCTA

- - - - - - - - - - - - - - - - - -ccccttt
- - - - - - - - - - - - - - - - - - - - - - - - - catgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg