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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttagcatatattgtttgctattggctgttttgattatcggaccacttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA

Basic information

species Glycine max
transcript GLYMA09G30410.1
intron # 6
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 6
lower sequence: AT5G44140.1 (Arabidopsis thaliana), 3'ss of exon 4
atttagcatatattgtttgctattggctgttttgattatcggaccacttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
        ||  || | |  | || |    ||| |  ||       || | |  | |||    ||  ||      ||||  || | |     ||  |||||||||||| || ||||| ||||| || || || |||||||| ||||||  |||||| || ||  |||||||||| ||||||||| |||||||||| || |
-------gtaggttatcttgtttttg----tttaagcattatgtgtctctggtttattagaagtt--gtgtgtaatgacaattatgt----gattcacagGGAGAAGCTAAGAGTGCTCAACTCATAGGGCAAGCTATTGCGAACAATGAAGCTTTCATTACTCTGAGGAAGATTGAAGCTGCAAGAGAGATTGCTCAGA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 5
atttagcatatattgtttgctattggctgttttgattatcggaccacttttgcatcttaagta-ttcagttct----ccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
              || |   |||||   | ||||||      | | |         | |||  ||  |  ||    |  |  |  || ||   |   ||  ||||||||||| |||||||| || || || ||||| || ||||| |||||||  || || |||||  |||| ||||| ||||||||  ||||||||||||| |
--------------gtatagcattggtgatcttgattgcaaatctaatgacatgagattagtggttttggcctgaagcattagctctttttgaatctttgtgcagGGAGAAGCTAAAAGTGCTCAGCTTATCGGACAAGCAATTGCGAACAATCAGGCATTCATCACTCTGAGAAAGATTGAAGCTGCGAGAGAGATTGCACAGA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 6
lower sequence: AT4G28510.1 (Arabidopsis thaliana), 3'ss of exon 5
atttagcatatattgtttgctattggctgttttgattatcggaccacttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
        || |  | ||         |    |  | |||  |  ||| |   | |  || | ||  ||    |   |  |  | |   |   ||   |||||||||| || ||||| || || ||||| || || ||||| ||||| | ||| ||||||||  | |||||||| || |||||| ||||||||||||| |
-------gtaaagagattctctacatttccacttgtaatctaa--actctgagagcgaaattgtt--gtgtgacgaaagttcacatggct---tgtgtagGGAGAAGCCAAGAGTGCTCAGCTCATTGGTCAAGCAATTGCAAACAACCAAGCGTTTATCACGCTCAGGAAGATCGAGGCTGCAAGAGAGATTGCACAGA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 6
-atttagcatatattgtttgctattggctgtt--ttgattatcggaccacttttgcatcttaagtattcagttctccctg-acctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
 ||||   |||  | ||||| | | | |   |  ||||   | ||  ||| ||  | | | |  ||   |  | |    | |      | ||| |  ||||||||| || || || |||||||| || || || || |||||||||||||||||||| || |||||  | || || || |||||| | ||||| ||||||||||
aatttcaaatac-tagtttgatttggacccctgattgagggt-ggttcacctt--cttttcagttacataaattttaaagtaagcaaatctctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

upper sequence: GLYMA09G30410.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 6
atttagcatatattgt-ttgctattggctgt-tttgattatcggaccacttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
 || ||  |   |    || || || | |    |  | ||| |  || ||| |   ||      ||  | ||        |   ||| ||| |  ||||||||| || || || |||||||| || || || || |||||||||||||||||||| || |||||  | || || || |||||| | ||||| ||||||||||
-ttgagggtggttcaccttcctcttagttacactcaaatattgtgccccttcttt-tcagtttcataaattttaagtaagcaaatctgtctctggtgaacagGGTGAGGCTAAGAGTGCCCAGCTGATAGGTCAAGCTATTGCCAACAATCCAGCATTCATCACGCTCAGAAAAATTGAAGCTTCCCGAGAAATTGCACATA

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|254318422|gb|GR832590.1|GR832590
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|58019484|gb|CX706226.1|CX706226
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|192332493|gb|FK024254.1|FK024254
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|192298739|gb|FG988605.1|FG988605
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|5753706|gb|AI960993.1|AI960993
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|26059988|gb|CA802902.1|CA802902
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACCG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCCACAATTCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|208264936|gb|GE063472.1|GE063472
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|151411498|gb|EV281309.1|EV281309
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|192325059|gb|FK016170.1|FK016170
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCA-CAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|298166390|gb|HO010969.1|HO010969
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
EST: gi|57574895|gb|CX547870.1|CX547870
EST:     TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAG                         GGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA
genomic: TTGTAGAAAAAGCTGAGCAAGACAAGAGAAGTGCTGTAATCAGAGCACAGgtgatgataa ... taatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA
                  ttcagttctccctgac  CT-rich tract
                                   tttctttctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttagcatatattgtttgctattggctgttttgattatcggaccacttttgcatcttaagtattcagttctccctgacctttctttctttaatgaacagGGAGAAGCAAAAAGTGCCCAACTAATTGGACAGGCTATTGCCAACAATCCAGCTTTTATCACATTGAGGAAGATAGAAGCTGCACGAGAGATTGCACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - -gcatata
- - - - - - -tgtttgc
- - - - - - - - - - - -tggctgt
- - - - - - - - - - - - - - - - - - - - - accactt
- - - - - - - - - - - - - - - - - - - - - - - - - tgcatct