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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggtttctcaataacctcaggtcttgatggttctgtcttgcaaagcactggtcttcttaatttgtttctgacttttaatagatgtgtttcttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG

Basic information

species Glycine max
transcript GLYMA16G22640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g38200.1 (Oryza sativa), 3'ss of exon 2
-------gggtttctcaataacctcaggtcttgatggttctgtct-tgcaaagcact-ggtcttcttaatttgtttctgacttttaatagatgtgtttcttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG
        | |||||  ||   | |||   ||   | |   || | |   |   ||| ||   | || ||||        || ||  |   ||||||| |       |||| || |||||||||||||| ||||| || || || || || ||||| ||||||||||||||||| |||||||| ||||
tgaaggatgttttcttgattgtcacagagttttcagatcaagtttgtttgattaactaggaacttttgatttagcat--gctcttgttttgtgtgtttgt-------agGTCACGCCAAATCTTTATGGCAATCTGGTGGCTAACACGGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G006672_T02 (Zea mays), 3'ss of exon 2
gggtttctcaataacctcaggtcttgatggttctgtc--ttgcaaagcactggtcttcttaatttgtttctg-acttttaataga------tgtgtttcttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG
    |||| ||   | |    ||  ||    | ||    || ||||    || | |  |||  ||   | || | ||| || | |      | || ||| | ||| ||||| ||||||||||||||||| ||||| || || |||   || ||||| ||||||||||||||||| |||||||| ||||
----ttctaaagggctttttttccagaataatatgaagatttcaaa----tgatttaattagattacctgtggagtttgaacatacttttctttggttccttttg-tagGTCACCCCAAATCTTTATGGCAATCTGGTGGCTAATGTAGCTGCAGGTATTGCTGGAGGCACTGGTGTCATGCCTGGAG

upper sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 2
-gggtttctcaataacctcaggtcttgatgg-ttctgtcttgcaaagcactggtcttcttaatttgtttctgacttttaatagatgtgtttcttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG
     | |  | || | |||    ||| ||  |||  | ||       |  |            | | | |  ||| |  |   ||   | | | || | |||| || || ||||||||||| ||| |||| |||||||| ||||| || |||||||| ||||| ||||||||||||||||
acctatgcctactagcttcattatttgttgtcttccatttttttccagagagaaaagaaagggct-tatatagcttatgctttgtggtgtacattttac-agGTGACACCTAATCTTTATGGCAATTTAGTGGCAAATACAGCAGCTGGTATTGCTGGTGGCACAGGAGTCATGCCAGGAG

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|6482120|gb|AW201391.1|AW201391
EST:     ATAACTGCTGTATGCAGCTTGGTTCAAAGCCTGAACAGGTTGATGTCATG                         GTTACCCCCAAATCTT-ATGGAAATCTAGTTGCAAATACTGCAGCAGGCAT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ttcttgctagGTTACCCC-AAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCAT
EST: gi|14259681|gb|BG882589.1|BG882589
EST:     GCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATT
genomic: GCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATT
EST: gi|7639494|gb|AW733816.1|AW733816
EST:     ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATG                         GTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATT
genomic: ATAACTGCTGTATGCAGCTTGTTTCAAAGCCTGAACAGTTTGATGTCATGgtatgtgtat ... ttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactggtcttcttaatttgtttctgacttttaatagatgtgtttcttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG
                                       tgtttcttcttgct  CT-rich tract
        ttcttaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggtttctcaataacctcaggtcttgatggttctgtcttgcaaagcactggtcttcttaatttgtttctgacttttaatagatgtgtttcttcttgctagGTTACCCCAAATCTTTATGGAAATCTAGTTGCAAATACTGCAGCAGGCATTGCTGGAGGCACTGGAGTCATGCCAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - cttgatg
- - - - - - - - - - - - - - - ttctgtc
- - - - - - - - - - - - - - - - - - - - caaagca