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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

Basic information

species Glycine max
transcript GLYMA19G30550.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctattttgctttggtaaaa----attgaaactttggactttgtttgtt--tagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
                         ||    |||   ||| |  |   |      || |  | |  | | ||||||     | | |        | ||      ||| ||  | ||   ||  ||| |   ||||| |||| || || ||||||||||| || |||||||| |||||||| || || ||  | || ||||| || || |||||||||||||||||||||||||
gttagtttccctctcttttctttgtgtgtatattcccctcttgctccccatgccccatctgcttaatccttttgtcctccttttgtcctccctttgaacttctgttgtaatctcggttattacttgctatcagATCTTGTTTGTCATATCAAAACCAGATGTCTTCAAGAGCCCAACATCAGATACATATGTCATTTTTGGCGAGGCAAAGATTGAAGACTTGAGCTCACAGC

upper sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S10_319V6.1 (Physcomitrella patens), 3'ss of exon 3
-gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
   || | |  ||    | ||||||  | | |    |  | | |  | | | | |   | | |  | || |     ||   ||    |   |    | |  ||||||| ||||| |||||    || || || |||||||| ||  |||| |||||||||||||| ||||| |||||||||||||| |||||||| || || |
aaatatc-tccgaactgtatttttcagtgtgcttatctgtgtctggtctctgaaaagcaatgtattctgttggc--ttacgaccaatgttgtaaaatttgcagATCCTCTTCGTGATCTCCGCTCCTGATGTGTTCAAGAGCCCTGCATCAGACACGTACATTATCTTTGGCGAAGCCAAGATTGAGGACTTGAGTTCTCAAC

upper sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctatt--ttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
    ||  ||  |  ||  ||||   ||  |        |  | ||||   || |   ||  ||  | ||     |||  |  || |||    |  |   | ||||  ||||||||||||| || || ||||| |||||||| ||| |||||||  |  |||| || ||||| || || |||||||| || ||||||||||| |
----gcgattctccaattgttttattttccccttgaatctggtgatttcgaagttagtttcgttattctgcctctaatgtatgctctggctgctaatgtatcagATTTTGTTCGTAATCTCGAAGCCTGACGTGTTCAAGAGCCCAGCATCTGATGCTCACATCATCTTTGGAGAGGCGAAGATTGAGGATTTGAGCTCACAAC

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|31463243|gb|CD405271.1|CD405271
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|193671194|gb|FK613274.1|FK613274
EST:     TCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|31474301|gb|CD416329.1|CD416329
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|193353181|gb|FK318445.1|FK318445
EST:     TGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|193418232|gb|FK383478.1|FK383478
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAA
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAA
EST: gi|31311589|gb|CD396792.1|CD396792
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCGAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|8827008|gb|BE210738.1|BE210738
EST:     GTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: GTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|298183956|gb|HO029169.1|HO029169
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|151407187|gb|EV277002.1|EV277002
EST:     CAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: CAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|193392741|gb|FK359236.1|FK359236
EST:     TGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|298198778|gb|HO042141.1|HO042141
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
EST: gi|31475951|gb|CD417979.1|CD417979
EST:     TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAAT                         ATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC
genomic: TGAAACCTGTCACAGGTGTCAGTCGAGTGACAGTCAAGAAGAGCAAGAATgttagcattt ... gtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC
                                         ctttgttt  CT-rich tract
                      taaaaattgaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcatttgactcatctttttcgcttttcaccaccctttttcatttgtcagatctattttgctttggtaaaaattgaaactttggactttgtttgtttagATCCTGTTCGTAATCTCAAAACCAGACGTTTTCAAGAGTCCAACATCTGACACGTACATTATATTTGGGGAAGCCAAGATTGAAGACTTGAGCTCACAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA