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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcgacaactttctcctttttttttgtggttcctcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA

Basic information

species Glycine max
transcript GLYMA15G16050.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G16050.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G472231_T01 (Zea mays), 3'ss of exon 1
---------------------gttagtttcgacaactttctcctttttttttg----tggttcctcgttttggattctgtttctgggtttgg--ttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
                       | | |  | |  ||| || |  |   ||||      ||  |||   |||    | | ||||  ||| ||  | |   |||     ||| |   |    | | ||    ||  | | |   |||||| || |||||| ||| | ||||||| ||  | |||||| | ||||||||||||||||| ||||  || |||||||| ||||| |||||||| || || |
gtaagaaccttatgcccttgctctcgctctgccttcttcctgcgctcgatttggtttccgtcgctccccttgttgaccggttcttcgttgggaatgggatttggccatttggggacttttctgtcgattccttctctg-tcggtcagGCATTCGAGAAGCACAGTATGGAGAAGGACATCGCGGAGTACATAAAGAAGGAGTTCGACAAGAACCACGGCCCCACCTGGCACTGCATCGTCGGCCGCA

upper sequence: GLYMA15G16050.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G15930.1 (Arabidopsis thaliana), 3'ss of exon 1
gttagtttcgacaactttctcctttttttttgtggttcctcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggattatt----cagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
                      |   ||  |     |    || | |     ||| | |||  | | || |   || | |  ||    |||| |  |||  |||| || |  ||  |    ||||||||||||||||||| ||||||||| ||| | || ||| | |||||||||||||| || ||||  |||||  | |||||||||||||| |||||||| |
--------------------aatcaattggttcaactaagagtctggtgaattgtctatggagt-gattatatgtg-tactctgatagataaggatttg--cattctgagatttgcttttgcagGCGTTTGAGAAGTACAGTGTGGAGAAGGATATAGCTGAGAATATAAAGAAGGAGTTTGACAAGAAACATGGTGCTACTTGGCATTGCATTGTTGGTCGCA

upper sequence: GLYMA15G16050.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv05s0077g02110.t01 (Vitis vinifera), 3'ss of exon 1
gttag-tttcgacaactttctcctttttt--tttgtggttcctcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggatt--attcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
||| | ||||     || ||   || |||   ||  | ||     |||||||   ||    |   |||  || |  || |||  |  | ||    | | |||   ||    | |||   | |||||| |  |||||  ||| |||||||||| |  |||||||| | || ||||||||||||||||||| |||||| || || ||||||||||| || ||||| |
gttggctttctttctctctcaatttctttggcttaggtttttattttttggaaaatggaaataa-tttacttcttttttctgtttgatttctgtgatttttggatatgggtctgatctcaatcagGCTTCGGAGAATCACAGTGTGGAGAAAAACATTGCGGAGTATATCAAGAAGGAGTTCGATAAGAAGCATGGACCTACCTGGCATTGCATTGTCGGTCGCA

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|207745416|gb|GD716344.1|GD716344
EST:     ATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: ATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|208162058|gb|GD960171.1|GD960171
EST:     CCGACATGATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|207702951|gb|GD686185.1|GD686185
EST:     TATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: TATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|193538987|gb|FK498167.1|FK498167
EST:     CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATAGTGGAGAAAGATGTTGCGGAGCAGATAAAGAA
genomic: CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAAT-GTGGAGAAAGATGTTGCGGAGCAGATAAAGAA
EST: gi|14126477|gb|BG790915.1|BG790915
EST:     CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|208322836|gb|GE118243.1|GE118243
EST:     CCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: CCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|193695451|gb|FK632075.1|FK632075
EST:     CCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: CCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|193673479|gb|FK617704.1|FK617704
EST:     CAGAAGGAGGCCGTTGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: CAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|254348898|gb|GR852577.1|GR852577
EST:     CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|208243692|gb|GE036991.1|GE036991
EST:     TATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: TATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|207770306|gb|GD742340.1|GD742340
EST:     ATCCCCGACATGCAGAAGGAGGCCGTTGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: ATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|207704819|gb|GD685522.1|GD685522
EST:     ATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
genomic: ATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG
EST: gi|193514540|gb|FK471094.1|FK471094
EST:     CCGACATGANCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCC                         GCGTTTGAGAAGTACAATGTGGAGAAAGACGTTGCGGAGCAGATAAAGAAG
genomic: CCGACATGATCCCCGACATGCAGAAGGAGGCCGTCGATATCGCCGTCGCCgttagtttcg ... gattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA
                             tcttgac  putative branch site (score: 3)
                                              attattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttcgacaactttctcctttttttttgtggttcctcgttttggattctgtttctgggtttggttgtgcttgctgcgttgtgtcataaagtcttgaccattttgcggattattcagGCGTTTGAGAAGTACAATGTGGAGAAAGATGTTGCGGAGCAGATAAAGAAGGAGTTCGATAAGAGGCATGGCCCCACTTGGCATTGCATCGTTGGTCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG