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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccttctcagttgatttgttatcacttacaagtgtctggccattgtttaagttctgttctggtgttgggagtaaaattgatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA

Basic information

species Glycine max
transcript GLYMA09G30410.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os07g15880.1 (Oryza sativa), 3'ss of exon 1
taccttctcagttgatttgttatcacttacaagtgtc-tggccattgtttaagttctgt---tctggtgttgggagtaaaattgatatgt--------tggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
             | |||| |  |  || |  |||    |   | |  || |||||  |    ||     | |  | |  | | |||| |        ||    || | ||||| || ||||| || |||||||| || ||||| ||||||||||||||  | || |||||||||||||| || ||| |||| || |||||||| ||||| |
------------agttttggtgccctttccttgtgctgcgcttaatacttcagttcaatccaccttaacatagctggatgactaatatatatttaacatgtactacctacagGTATACCCTGAGGGGACTCACTTTATGATTCCATGGTTTGAGAGGCCAATCATTTATGATGTCCGTGCTCGTCCCAATCTTGTGGAGAGTACTTCTGGAA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g62490.1 (Oryza sativa), 3'ss of exon 1
---------------taccttctcagttgatttgttat----cacttacaagtgtctg----gccattgtttaagttctgttctggtg--ttgggagtaaa---attgatatg-ttggttaac------gtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
                | | |   |||  | |||| ||      |  |   || || |    || ||   |    || || | |||||  ||| |  | ||   |||| | || ||||||         |||||||| || ||||| || ||||||||||| || |||||||| ||||||||| | ||||| |||||||| || || ||| | || || ||||| || ||||| |
gtaacccatcgatcgaagcctactagtgaacttgtgatgtgatgccgatgggtttcagagaagctatgcgtgtgcttgtgatttggtgggttgcgtttgaatgaattgttgtggttggttgtgtgctcggtgcagGTGTACCCTGAGGGGACTCACTTCATGATCCCGTGGTTCGAGAGGCCGATCATCTACGATGTCCGAGCCCGCCCCAACCTCGTCGAGAGCACTTCTGGAA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 3'ss of exon 2
taccttctcag-ttgatttgttatcacttacaagtgtct--ggccattgtttaagttctgttctggtgttgggagtaa--aattgatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
      || ||  ||||| || || |  |     |||    |   |  ||  ||    | ||||    |    ||||   |  |  ||   | ||||    |||||| || ||||| || || ||| | || ||||| |||||||| |||||||| |||||||| || ||||| |||||  | || |||||||||||||| || |
-----cctgagactgattagtcatgaaattttgttgttctcgttgagcgtaaaaacagtcttcttaattcacaagtatgtagcttgtaaccttgttattacgcagGTTTACCCTGAGGGTACACACCTTATGATTCCTTGGTTTGAAAGGCCGGTCATCTATGACGTTCGTGCTCGACCTTACCTTGTTGAGAGTACATCCGGAA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 3
taccttctcagttgatttgttatcacttaca-agtgtctggccattgtttaagttctgttctggtgttggg-agtaaaat-tgatatgttggtta-acgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
    || ||  ||  |   | |  | ||    | | ||||    |  | |   || |  |     ||     | || ||  | |||  ||  |   |  ||||||| |||||||| || |||||| | || || || |||||||| ||||| ||||||||||||||||||||||| || ||||| || |||||||| || ||||
----ttttcttttcctgcatcactaattctgtaatttctgtttttcctgttgtttgtcattcaccgtaactcattagaacatcatactttcatgggatatgcagGTTTATCCTGAGGGGACTCACCTGATGATCCCATGGTTTGAAAGGCCAGTTATCTATGATGTCCGTGCACGCCCTCATCTGGTGGAGAGTACTTCAGGGA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 3
-taccttctcagttgatttgttatcacttacaagtgtctggccattgtttaagttctgttctggtgttgggagtaaaattgatatgttggtta-acgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
     |  |    ||  |   ||   ||   |  | | |      | |||  ||  |   |||   ||      || ||  |||  | | |   |  ||||||| ||||| || ||||||||| | || || || |||||||| ||||| || ||||||||||||||| | || || ||||| || |||||||| || ||||
gagtttcttttcctgcatcactaattctgtaatttatgtttttcctatttt-gtcattcactgtaattcattagaacatc-atacttagatgggatatgcagGTTTATCCCGAGGGAACTCACCTGATGATCCCATGGTTTGATAGGCCAGTCATCTATGATGTCCGTACGCGCCCTCATCTTGTGGAGAGTACTTCAGGGA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S41_59V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------taccttctcagttgatttgttatcacttaca-agtgtctggccattgtttaagttctg--ttctggtgttgggagtaaaattgatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
             |   |    | |  ||| ||  |   | | |  |  | |||   |  |||| | | ||  || ||  | | |  |   | ||     |  | |   | ||||||| ||||| || ||||| || || || ||||| ||||| || ||||| || || ||||||||||||||||||||  |  | || ||||| || || ||||
gtgagtgagtgagtgagtgtgaattgcattggtctttgatgagacggaatttggatttgttttagggtttggattttgacgatcgtggcggattt----cgaggatggccttgcagGTGTATCCAGAGGGAACGCATTTTATGATTCCCTGGTTCGACAGGCCTGTGATATATGATGTCCGTGCACGACCTAACATTGTCGAGAGCACGTCGGGGA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S14_33V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------taccttctcagttgatttg-ttatcacttacaagtgtctggccattgt-ttaagttctgttctggtgttgggagtaaaattgatatgttggttaacg--tgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
                                   |    | ||| |||  ||| || | |  |     | | |     |||  || ||| | |||  ||| ||   | |      |   | | ||| | ||  ||||||| |||||||| ||||| || || || ||||| |||||||| || || || || || |||||||||||||||||| |  | || || || ||||| || |
gtgcgggagggtgaattgaagtgggttagttgttttgttctttcaattggattgattgttaagtttggttttgtaaggtttgggttgagtccggttggggtttttataatcgtgccgg-gtttcggtgatcggttgcagGTGTATCCTGAGGGAACGCATTTTATGATTCCCTGGTTTGACAGACCTGTGATATACGATGTCCGTGCACGACCCAACATTGTCGAAAGCACATCAGGAA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ20024 (Selaginella moellendorffii), 3'ss of exon 1
taccttctcagttgatttgttatcacttacaagtgtctggccattgtttaagttctgttctggtgttgggagtaaaatt-gatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
         ||  ||  |  |  | |   ||      ||  |  | ||| | ||| |   | |   |    ||| | || |||   |   ||  | | ||||||||||| |||||||| || || ||  | ||||||||||| ||||| || ||||| |||||||||||  ||||| |  | || |||||||| ||||| |
-------gtaggcgagct--tgccgcaagcatcgcattgctctctcttttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCTGGCA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ07463 (Selaginella moellendorffii), 3'ss of exon 1
taccttctcagttgatttgttatcacttacaagtgtctggccattgtttaagttctgttctggtgttgggagtaaaatt-gatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
         ||  ||  |  |  | |   ||      ||  |  | ||| | ||| |   | |   |    ||| | || |||   |   ||  | | ||||||||||| |||||||| || || ||  | ||||||||||| ||||| || ||||| |||||||||||  ||||| |  | || |||||||| || || |
-------gtaggcgagct--tgccgcaagcatcgcattgctctctcttttatttcggggatcgccctttttgtagagttcgattgatcttttgccttccagGTCTATCCCGAAGGAACGCATTTGATGGTGCCGTGGTTTGACAGGCCAGTGATCTACGATGTCCGTGCTAGACCCAACTTGGTCGAGAGTACTTCCGGCA

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|26059988|gb|CA802902.1|CA802902
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|33388681|gb|CA851888.1|CA851888
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|193508459|gb|FK465742.1|FK465742
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|151410209|gb|EV280024.1|EV280024
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|151411498|gb|EV281309.1|EV281309
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCTGATT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|192325059|gb|FK016170.1|FK016170
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|254318421|gb|GR832589.1|GR832589
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|208045995|gb|GD847739.1|GD847739
EST:     GAGGTCACCGAGCCATTATTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTT
EST: gi|192332492|gb|FK024253.1|FK024253
EST:     GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAG                         GTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGA
genomic: GAGGTCACCGAGCCATTGTTTTCAACCGTCTAGTTGGTGTCAAAGACAAGgttattatat ... taacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttaagttctgttctggtgttgggagtaaaattgatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA
                                          ggttaac  putative branch site (score: 3)
                           taaaattgatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccttctcagttgatttgttatcacttacaagtgtctggccattgtttaagttctgttctggtgttgggagtaaaattgatatgttggttaacgtgcagGTCTATCCTGAAGGAACTCACTTCATAATTCCGTGGTTTGAGAGGCCGGTTATCTATGATGTCCGTGCACGACCCCATCTAGTTGAGAGTACATCTGGGA

- ccttctc
- - - - - - tgatttg
- - - - - - - - - - - -cacttac
- - - - - - - - - - - - - - - - - - ctggcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatatg