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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcctcttgtctacttttgtaacttgctaattttcacatttttttaaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG

Basic information

species Glycine max
transcript GLYMA10G02040.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 15
------gtaagtgtcctcttgtctacttttgtaacttgctaattt-tcacattttttt--------aaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
      | || |   |  || | ||   ||  |  |  ||  | | | |||| |  ||          | ||| ||||  ||||      | ||||||||||| |||||||| || ||||| ||||| |||| ||| |||||||| ||  | ||  | |||
gtaagtgaaattcatccattttgtagccttacatttatcttttctattacatctgctttcgtgagtgcatacttaattctatttaataaatgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCACACAAAGAAGGAAGCACATTGAAG

upper sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 15
----gtaag-tgtcctcttgtctacttttgtaacttgctaattttcacatttttttaaaaactgaatttaatttgt---ctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
    ||||  ||     ||  ||  |||    |  || |  |  |   |     |    | |     ||| ||| |   |  || ||||||||||| |||||||| || ||||| ||||| |||| |||||||||||| ||    ||  | |||
gtaagtaaaatgaaaatttaccttttttaaatatctgtttgtggttgtaaaaagtagtgagccatgcttactttttgaacgattgcagAAAATTGGCTATGACAATGCTGCAGCTGTTGCTAAGAAAGCCCACAAAGAAGGAACCACGTTGAAG

upper sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 16
------------------------------gtaagtgtcctcttgtctacttttgtaacttgctaattttcacatttttttaaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
                               ||    |||  ||  | | |    | |||    ||| | |     |  | |      ||||     |  ||| | ||||||||| || |||||||| || |||||||||||||||| ||| |||||||| || |||||  | |||
gtaagtctctaaatattgaactccgcctttttagtcatccgttttaccattaggattactaatgaatgtactttgatgctgagttttggaatccttatcctctttaccagAAAATCGGGTATGACAATGCTGCAGCAGTTGCCAAGAAAGCTCACAAAGAAGGATGTACATTGAAG

upper sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G50950.1 (Arabidopsis thaliana), 3'ss of exon 15
gtaagtgtcctcttgt----ctacttttgtaacttgctaattttcacatttttttaaaaactgaattta-----------atttgtctgtt-ccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG----------------------------------
|||||| ||    | |    || ||||   || |     || ||| |||| |  | | || ||||||||           |||  ||  || |||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || ||  | |||                                  
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAGGTAAACAATAAACTATTAACGTTTTCATCACTAA

upper sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 15
gtaagtgtcctcttgt----ctacttttgtaacttgctaattttcacatttttttaaaaactgaattta-----------atttgtctgtt-ccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
|||||| ||    | |    || ||||   || |     || ||| |||| |  | | || ||||||||           |||  ||  || |||||||||||| |||||||| || |||||||| ||||| | ||| |||||||| || || ||  | |||
gtaagtctctaaatattaaacttctttgtcaagtcatccatattctcattatgattacaaatgaatttacctcaatgctaattcctcctttaccagAAAATTGGCTATGACAATGCTGCAGCAGTAGCCAAAAGAGCTCACAAAGAAGGATGCACATTAAAG

upper sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 16
----gtaagtgtcct---cttgtctacttttgta-acttgctaattttcacatttttt-taaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
    ||   ||| ||   | ||| | | ||  || ||||    |||       | |    || |||| |   |  |   |||||| ||||||||||||||||| || || || || |||||||||| |||||| || |||||  | ||||| |||
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|254343541|gb|GR857297.1|GR857297
EST:     TCACTGATGCTCGTCACATCCTTAAACCCA                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTGATGCTCGTCACATCCTTAAACCCAgtaagtgtcc ... tctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|254343540|gb|GR857296.1|GR857296
EST:     TCACTGATGCTCGTCACATCCTTAAACCCA                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTGATGCTCGTCACATCCTTAAACCCAgtaagtgtcc ... tctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|58014928|gb|CX701670.1|CX701670
EST:     TCACTGATGCTCGTCACATCCTTAAACCCA                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTGATGCTCGTCACATCCTTAAACCCAgtaagtgtcc ... tctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|209708984|gb|BW653498.1|BW653498
EST:     TCACTGATGCTCGTCACATCCTTAAACCCA                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
genomic: TCACTGATGCTCGTCACATCCTTAAACCCAgtaagtgtcc ... tctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG
EST: gi|193401454|gb|FK369277.1|FK369277
EST:     TCACTGATGCTCGTCACATCCTTAAACCCA                         AAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAGGAG
genomic: TCACTGATGCTCGTCACATCCTTAAACCCAgtaagtgtcc ... tctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttgctaattttcacatttttttaaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG
                                             tctgttcc  CT-rich tract
        taattttcacattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcctcttgtctacttttgtaacttgctaattttcacatttttttaaaaactgaatttaatttgtctgttccagAAAATTGGTTATGACAAGGCAGCAGCAGTTGCCAAGACAGCCCACAAAGAGGGGTGTACTCTTAAG

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