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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagttaccatatttcttcatcttagtgtaattaaggttattgctacaatacaagttttatgaacatatcaaacatataatgtcaacaattaccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGA

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 8
ttagttaccatatt-tcttcatcttagtgtaattaaggttattgctacaatacaagttttatgaacatatcaaacatataatgtcaacaattaccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGA
          |||  | ||| |  |    |  ||  ||       ||||  |    ||| || | |   ||||| | || |||||     |    ||  |||||||||| ||||| ||| |||| || ||  |||||||| | |  ||||||||||||||||| ||||| || |||||||| || |||||||| ||||| |
---------gtatggttttctttgtgagatctttgtggcagaatatacataattgttttcatta-ctggtcaaaaa-atgatgtc-----tcctgctatagGCATTGGCGAGCACGCTTGATGATGAGGAACTGGCTGATCTTAGGGATCAATTTGATGCTATCGATGTGGATAAAAATGGCTCTATTAGCCTTGAAGAAA
















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|208136736|gb|GD939696.1|GD939696
EST:     ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGG                         GCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAG
genomic: ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGGgtaagagaaa ... taccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAG
EST: gi|193364409|gb|FK328914.1|FK328914
EST:     ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGG                         GCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAA
genomic: ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGGgtaagagaaa ... taccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAA
EST: gi|193432383|gb|FK394769.1|FK394769
EST:     TGAAATATAGTCGATTCAAACAAATTTGCACTGAGG                         GCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAAGATCA
genomic: TGAAATATAGTCGATTCAAAC-AATTTGCACTGAGGgtaagagaaa ... taccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATAT-AAAAGATCA
EST: gi|207825702|gb|GD797329.1|GD797329
EST:     ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGG                         GCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAG
genomic: ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGGgtaagagaaa ... taccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAG
EST: gi|208085782|gb|GD880636.1|GD880636
EST:     ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGG                         GCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAG
genomic: ACATGCGGCAGTTTGTGAAATATAGTCGATTCAAACAATTTGCACTGAGGgtaagagaaa ... taccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatacaagttttatgaacatatcaaacatataatgtcaacaattaccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGA
                                            ttaccct  CT-rich tract
                    atatcaaacatataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagttaccatatttcttcatcttagtgtaattaaggttattgctacaatacaagttttatgaacatatcaaacatataatgtcaacaattaccctgcagGCATTGGCTAGCACACTTAATGAAGAAGAGTTGGCTGATATAAAAGATCAATTTGATGCTATAGATGTAGACAAAAATGGTTCGATTAGCCTGGAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA