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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttgcaaactactaaaattgttctcataatgacttagaaggatgggaaagctcgtaatatggaatccttctctcatttgattaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCTATGTTTGCTACCTTTTGCATCATGGCAG

Basic information

species Glycine max
transcript GLYMA07G09270.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G09270.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G412899_T04 (Zea mays), 3'ss of exon 12
ttctttgcaaactactaaaattgttctcataatgacttagaaggatgggaaagctcgtaatatggaatcctt--ctctcatttgattaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCTATGTTTGCTACCTTTTGCATCATGGCAG
   ||| |    | |  |   | |||  | |   |  |    | |  ||    ||| |  |||  | || ||  |   || |   | ||||    |   ||| |  | || ||||||||| |  |  ||||||||||| | |||||| |||||||||||||||| || ||| | || ||| |  |  | ||  |  | ||  
--gttttcctctttcctatgcttttcgtagatccagctttcggcactgggtttctctttttatacactcattgacatccaatctttgaatgtaacttggcagATCGTGAACTTCTTTGTTAGTTTGATGTTCTTGCGTCTTCTGGAGCAACTTGGTCCACAGCTTCTCTACACAATATTTTCGTCAGTCTGTGTGGTAGCCT

upper sequence: GLYMA07G09270.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv11s0016g03660.t01 (Vitis vinifera), 3'ss of exon 13
ttctttgcaaactactaaaa-ttgttctcataatgacttagaaggatgggaaagctcgtaatatggaatcc-ttctctcatttgattaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCTATGTTTGCTACCTTTTGCATCATGGCAG
     |  |      || |  ||| | ||| | | |      |   ||    ||||   ||| |   ||   |||  |   || | |||  ||||| | |||||||||||||||||||| ||  | || ||| ||| |||||||||| ||||||| ||||||||  | ||||||||||||  |||||||||| | |||||||
--tgctaaatgtaggtagaccttggtatcaaatttataactgaatctgaatgagcttccaatttcttatttgttcatttggttcaataactgtcttctccagGTGATAAATTTCTTTGTGGGCTTGCTCTTCCTGCCTTTGCTGGAGCAACTTGGACCACAGCTCTTGTACTCTATGTTTTGTACCTTTTGCTTGATGGCAG
















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|58018453|gb|CX705195.1|CX705195
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|192327720|gb|FK021355.1|FK021355
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|19346368|gb|BM891248.1|BM891248
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|21595709|gb|BQ610581.1|BQ610581
EST:     CAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|8284412|gb|BE021971.1|BE021971
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|10231460|gb|BE800348.1|BE800348
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|192322087|gb|FK012191.1|FK012191
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|15286792|gb|BI470683.1|BI470683
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|21256350|gb|BQ453238.1|BQ453238
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|151399677|gb|EV269548.1|EV269548
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|15664632|gb|BI702003.1|BI702003
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|254319872|gb|GR830896.1|GR830896
EST:     ATGTCAGTGCATTGG                         GTGATAAATTTCCTTTGTTGGACTACTG-TCCTGCGTTTGCTGGAGAAACT
genomic: ATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTT-CTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACT
EST: gi|192322086|gb|FK012190.1|FK012190
EST:     TCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: TCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|254339875|gb|GR858000.1|GR858000
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|17023662|gb|BM094696.1|BM094696
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTG
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTG
EST: gi|58017137|gb|CX703879.1|CX703879
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|192333446|gb|FK023975.1|FK023975
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|8284214|gb|BE021773.1|BE021773
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|192333445|gb|FK023974.1|FK023974
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
EST: gi|19346670|gb|BM891550.1|BM891550
EST:     CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGG                         GTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT
genomic: CTAGTCGAATAAGAGCCAAAGCCATGGCAGTCTGTATGTCAGTGCATTGGgtaattttct ... tcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggaaagctcgtaatatggaatccttctctcatttgattaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCTATGTTTGCTACCTTTTGCATCATGGCAG
                                    gattaat  putative branch site (score: 3)
                                atttgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttgcaaactactaaaattgttctcataatgacttagaaggatgggaaagctcgtaatatggaatccttctctcatttgattaatggtcttgtacagGTGATAAATTTCTTTGTTGGACTACTGTTCTTGCGTTTGCTGGAGAAACTTGGTCCACAGCTGCTTTACTCTATGTTTGCTACCTTTTGCATCATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT