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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattatatcttgatctctattagagatgacaatttgtccgttgatggcaataaattaaaaggaaaaagagcaataatttatttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG

Basic information

species Glycine max
transcript GLYMA07G36610.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g61710.1 (Oryza sativa), 3'ss of exon 4
gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattatatctt-gatctctattagagatgacaatttgtccgttgatggcaataaattaaaaggaaaaagagcaataatttatttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG
                                                                           ||||| || ||| | |  |   |       ||         ||   ||  |  | ||     | |          || || | |  | |  ||| |||||||| |||||||| |||||||||||||| ||| | ||||||||||| ||||  | | ||||    || ||||| |||
--------------------------------------------------------------------------gtatatttttgatattttgttttgggattctttcacttccaaataataagcatgttaagtttgacatgattgcgtgttgtt-actcttatgtagGATCTGGACTTTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAGTTCTTGAGAAAAATTTCCCAAAG

upper sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G458549_T02 (Zea mays), 3'ss of exon 4
gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattatatcttgatctctattagagatgacaatttgtccgttgatggcaataaattaaaaggaaaaagagcaataatttatttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG
                                                                          ||  || | |  ||   || |   |   ||| | ||| |   ||   ||   ||| ||  | ||||         |  | | | || |   ||| |||||||| |||||||| |||||||||||||| ||| | ||||||||||| ||||      ||||    ||||| || |||
-------------------------------------------------------------------------gtttgatttagtgct---ttgggtgtacaaatatatccttc--tgttcatgt-ttataaaaataaaggattgctgctgttatttctcctgttagGCTCTGGACTGTCAAGCTCAGCAGCATTTGTCTGTTCAGCAACAATTGCTATCATGGGAATCCTTGACAAAAACTTTCCAAAG

upper sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G06580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattatatcttgatctctattagagatgacaatttgtccgttgatggcaa-taaattaaaaggaaaaagagcaataatttatttatttc--tttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG
                                                                       |   |  ||| ||||   ||    | |  | || || ||  || |    || |  || |           |||  ||| |    | | ||  |||  |||||||||  | ||||| ||||| |||||||| |||||| | |||||||||||||||||||  |||| |   |||||   ||||
----------------------------------------------------------------------gtatatgcatcatgatacttacggaacagaaaaacttatcatttcaaataaagtttatcagtttactttcaagctgtaactggagtgtctcgatttttagGTTCTGGGTTGTCAAGTTCTGCTGCATTTGTTTGCTCAGCAACAATTGCTATTATGGCTGTCTTTGGTCATAACTTTGAGAAG

upper sequence: GLYMA07G36610.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattat-atcttgatctctattagagatgacaatttgtccgttgatggcaataaattaaaaggaaaaagagcaataatttat-ttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG
                                                                 | | | |   ||| || || || | ||      ||| || | | |   |||  |  | |   ||      |  | ||    | | | |  ||||||   |||||| |||||||||||||||||||| |||||||| |||||||| |  |||||||| |||||||||| |||||| | |||||| |||
----------------------------------------------------------------gtttagtttcctatcattttcatgtataaggacaatgtcactgt-tattttggggtaactctcttccttatagtatgaagtttgagtcacattattttcctacagGATCTGGACTATCAAGCTCTGCGGCATTTGTTTGCTCATCTATGATTGCTATAATGGCTGCTTATGATGTCAGCTTCCCAAAG

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|209713259|gb|BW684346.1|BW684346
EST:     TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAG                         GTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTA
genomic: TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAGgtgtgttcat ... ttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTA
EST: gi|7146072|gb|AW507994.1|AW507994
EST:     TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAG                         GTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTA
genomic: TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAGgtgtgttcat ... ttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTA
EST: gi|213589192|gb|DB957724.1|DB957724
EST:     TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGGACAGTGCCGACAG                         GTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCAT
genomic: TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAGgtgtgttcat ... ttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCAT
EST: gi|213603198|gb|DB960461.1|DB960461
EST:     TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAG                         GTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTA
genomic: TGGCAAACCTGTTGGACTTGAAGTTCTTGTTGATGGAACAGTGCCGACAGgtgtgttcat ... ttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatggcaataaattaaaaggaaaaagagcaataatttatttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG
 cgttgat  putative branch site (score: 5)
                                    tttatttatttcttt  putative PPT
        aataaattaaaaggaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgttcattagttttgaattagaatggtgctgctaaggacatgtaaatttacctctaagttaatgttgatcattatatcttgatctctattagagatgacaatttgtccgttgatggcaataaattaaaaggaaaaagagcaataatttatttatttctttacagGTTCTGGACTATCAAGCTCTGCAGCATTTGTCTGCTCATCCACAATTGCTATTATGGCTGCTTTTGATGTGAACTTCCCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT