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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcctcttgtcttctccggtaacttgctaattttcacatattttttaaacggaattgaatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG

Basic information

species Glycine max
transcript GLYMA02G01920.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
gtaagtg--------tcctcttgtcttctc-cggtaacttgctaattttcacatattttt-------taaacggaattgaatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
|||||||         | | ||||   ||  |  | |  |  |   || ||  |  |||         | ||  ||||  ||||      | ||||||||||| |||||||| || ||||| ||||| |||| ||| |||||||| ||  | ||  | |||
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
----gtaag-tgtcctcttgtcttctccggtaacttgctaat--tttcacatattttttaaacggaattgaattt--gcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
    ||||  ||     ||  ||| |      |  || |  |  ||  | | | |  | |  |    ||   |||    |  || ||||||||||| |||||||| || ||||| ||||| |||| |||||||||||| ||    ||  | |||
gtaagtaaaatgaaaatttaccttttttaaatatctgtttgtggttgtaaaaagtagtgagccatgcttactttttgaacgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 16
------------------------------gtaagtgtcctcttgtcttctccggtaacttgctaattttcacatattttttaaac-ggaattgaatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
                               ||    |||  ||  |   |  | | |||    ||| | |    ||  |       |||||     |   || |  |||||||| || |||||||| || |||||||||||||||| ||| |||||||| || |||||  | |||
gtaagtctctaaatattgaactccgcctttttagtcatccgttttaccattaggattactaatgaatgtactttgatgctgagttttggaatccttatcctctttaccagAAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAG

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaagtgtcctcttgt----cttctccggtaacttgctaattttcacatatt--ttttaaacggaattg-----------aatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG----------------------------------
|||||| ||    | |    |||||  |  || |     || ||| |||  |  ||  ||| | | ||            | |   ||| |  ||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || ||  | |||                                  
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaagtgtcctcttgt----cttctccggtaacttgctaattttcacatatt--ttttaaacggaattg-----------aatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
|||||| ||    | |    |||||  |  || |     || ||| |||  |  ||  ||| | | ||            | |   ||| |  ||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || ||  | |||
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG

upper sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 16
gtaagtgtcctcttgtcttctccggtaacttgc-taattttcacatatt---ttttaaacggaattgaat----ttgc--ctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
|| ||| ||   |      ||  | | | |     | || ||   || |    | |  ||   |    ||    ||||  ||||||||||||||||||||||| || || || || |||||||||| |||||| || |||||  | ||||| |||
gtgagtttctgttctatccctgtgttcattcctacacttctcgattactgtgctctggacaataacttatgctgttgcttctgtttcagAAAATTGGTTATGATAATGCCGCTGCTGTTGCCAAGAAAGCCCATAAGGAGGGAAGGACTCTGAAG

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|192310777|gb|FK000291.1|FK000291
EST:     TCACTAATGCTTGTCACATCCTTAAACCCG                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTAATGCTTGTCACATCCTTAAACCCGgtaagtgtcc ... cctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|193666295|gb|FK611808.1|FK611808
EST:     TCACTAATGCTTGTCACATCCTTAAACCCG                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTAATGCTTGTCACATCCTTAAACCCGgtaagtgtcc ... cctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|192310922|gb|FG998898.1|FG998898
EST:     TCACTAATGCTTGTCACATCCTTAAACCCG                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTAATGCTTGTCACATCCTTAAACCCGgtaagtgtcc ... cctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|209717304|gb|BW659019.1|BW659019
EST:     TCACTAATGCTTGTCACATCCTTAAACCCG                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTAATGCTTGTCACATCCTTAAACCCGgtaagtgtcc ... cctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaacttgctaattttcacatattttttaaacggaattgaatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
      tgctaat  putative branch site (score: 2)
                                             cctgtttc  putative PPT
         taattttcacatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcctcttgtcttctccggtaacttgctaattttcacatattttttaaacggaattgaatttgcctgtttcagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG