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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaccccccaaaggacacctcggaatcctattcaatggacatttcgtggtgtatgctattctttgttccttgctcacgaggtatgttttgtgttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG

Basic information

species Glycine max
transcript GLYMA15G04300.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04300.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g04700.t01 (Vitis vinifera), 3'ss of exon 3
gaccccccaaaggacacctcg----gaatcctattcaatggacatttcgtggtgtatgctattctttgttccttgctcacgaggtatgttttgtgttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
      | | |  | | ||      | |  || | ||  | |    |  || | ||   |||       ||     | || |   |   ||    ||   |||||||||||||||||| ||||||| || ||||||||
----tacaagattaaatcttatagaggactctgtccatagaatgaattttgttctaaaatatgaccatctctgacttgactaatgaaaattaccattaccgcagTTGAAGAAGATGTGCAAAGAAGCTGCATATTGGG
















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|208292044|gb|GE094244.1|GE094244
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|151394173|gb|EV264044.1|EV264044
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|192294632|gb|FG986481.1|FG986481
EST:     GGAATATCTCAAGTCATGATTTCGAGAAAACG                         TTGAAGAAGATGTGCAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|209724919|gb|BW669608.1|BW669608
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|26267988|gb|CA819051.1|CA819051
EST:     ATTTCGAGAATACT                         TTCAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: ATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|151401884|gb|EV271697.1|EV271697
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|151402473|gb|EV272286.1|EV272286
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|209720222|gb|BW674562.1|BW674562
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|209720223|gb|BW674563.1|BW674563
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|31468370|gb|CD410398.1|CD410398
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|209697438|gb|BW675583.1|BW675583
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|31463245|gb|CD405273.1|CD405273
EST:     GGAATATCTCAAGTCGTGATTTCGAGTAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|254344722|gb|GR851312.1|GR851312
EST:     GGAATATCTCAAGTCATGATTTCGAGAAAACG                         TTGAAGAAGATGTGCAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|151397154|gb|EV267027.1|EV267027
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|192306327|gb|FG995107.1|FG995107
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|209697437|gb|BW675582.1|BW675582
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|207830761|gb|GD803699.1|GD803699
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTAGGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATT-GGGG
EST: gi|31474890|gb|CD416918.1|CD416918
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|192306328|gb|FG995108.1|FG995108
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|193329078|gb|FK293082.1|FK293082
EST:     ATTTCGAGAAAAC-                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: ATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|209724918|gb|BW669607.1|BW669607
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|31468248|gb|CD410276.1|CD410276
EST:     GGAATATCTCAAGTCGTGATTTCGAGAAAACT                         TTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
EST: gi|193397507|gb|FK361525.1|FK361525
EST:     GGAATATCTCAAGTCATGATTTCGAGAAAACG                         TTGAAGAAGATGTGCAAAGAAGGTGTATATTGGG
genomic: GGAATATCTCAAGTCGTGATTTCGAGAAAACTgtaagttcgc ... gttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgtatgctattctttgttccttgctcacgaggtatgttttgtgttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG
                        tgctcac  putative branch site (score: 2)
          tattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaccccccaaaggacacctcggaatcctattcaatggacatttcgtggtgtatgctattctttgttccttgctcacgaggtatgttttgtgttgttgcagTTGAAGAAGATGTGTAAAGAAGGTGTATATTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
-acccccc
- - - - - - - cacctcg
- - - - - - - - - - - - - ctattca
- - - - - - - - - - - - - - - - - - - - - - - - -gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtatgt