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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catttcctttttgcttgagtttacaagttattagttctgctatcaatattcatttttgcgtgtttgtactgacatgtgatgctcttctaaaaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGGTATTGGGTATCTGTGATTGTTAAGAGAATAGTGAGATTTTGTTAATTTA

Basic information

species Glycine max
transcript GLYMA14G17930.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G17930.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 5
catttcctttttgcttgagtttacaagttattagttctgctatcaatattcatttttgcgtgtttgtactgacatgtgatgctcttctaaaaatatg---cagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGA-TTTTGAGAGTTTGGTA--TTGGGTATCTGTGATTGTTAAGAGAATAGTGAGATTTTGTTAATTTA
   |    | ||     |  |   |    |  ||||    ||| | | |       ||      | || | |  ||   |  | |  |  || | ||   ||||||||| ||||| || ||||||||||||||||| ||| |||||  || | |||   |||  |||    |    |   | | ||  | ||  | ||||| ||| 
--atgatgtgttatccaatctgggactaaaacagttgatttattactgtcataccctgaacacctctaat-atttgcctttttttggtggaattttgttgcagAAATGGTCTTAGAGAGCGACGCAGAAGCAGAAGCTGAGTTTTGCAAGCTCGGTGACTTGACTATTGAGGGGAATACTGGGCATT-TAAG--TGTGTTAGTTTG
















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|58025100|gb|CX711841.1|CX711841
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGG--A-                         AA-TGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|254321482|gb|GR824799.1|GR824799
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAAT--G--G                         AAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|6726506|gb|AW310860.1|AW310860
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAAT--G--G                         AAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|192324562|gb|FK016453.1|FK016453
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGG--A-                         AA-TGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|151395696|gb|EV265573.1|EV265573
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGG--A-                         AA-TGGCCTTAGGGAACGACGCATAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|9983911|gb|BE658019.1|BE658019
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGG--A-                         AA-TGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|192295485|gb|FG987099.1|FG987099
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGG--A-                         AA-TGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|21675883|gb|BQ628234.1|BQ628234
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAAT--G--G                         AAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|192300160|gb|FG989282.1|FG989282
EST:     GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGG--A-                         AA-TGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
EST: gi|6073116|gb|AW102503.1|AW102503
EST:     GGTCTTCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAAT--G--G                         AAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG
genomic: GGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTAATGGGTAGgtttcttctg ... aaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattcatttttgcgtgtttgtactgacatgtgatgctcttctaaaaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGGTATTGGGTATCTGTGATTGTTAAGAGAATAGTGAGATTTTGTTAATTTA
                                     tcttctaaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catttcctttttgcttgagtttacaagttattagttctgctatcaatattcatttttgcgtgtttgtactgacatgtgatgctcttctaaaaatatgcagAAATGGCCTTAGGGAACGACGCAGAAGCAGAAGTTGATTTTGAGAGTTTGGTATTGGGTATCTGTGATTGTTAAGAGAATAGTGAGATTTTGTTAATTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA