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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatatttatctgctggtcttgttttgaatttgtatgagttgtctcttctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG

Basic information

species Glycine max
transcript GLYMA06G13210.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13210.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G060896_T02 (Zea mays), 3'ss of exon 7
----------------------------------------------gtatatatt-tatctgctggtcttgttttga-atttgta--tgagttgtctcttctgtggctttagtttgtt--gattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG
                                               |||||  | || || || || |  ||| || ||| |||  | | |  ||  ||||    || || |||     || || ||||  | | | |||  ||||||| || ||  | | |   |||||||||||||  |||||||| || ||||||||||| ||||||||| | |
gtatgtagataattccatgaggctatgatgactacattattttctgatatatgctgtagcttcttgtttcttttagatattggtaaataaatactcagttcttgaactgtaatttcacaagaattgttttttatctacttt--cagCTGTGGAGTTCTTGAGAAATGCTCCTGAAGGGACATATGATGCTATCATTGTTGATTCGTCAGATCCAATAG

upper sequence: GLYMA06G13210.2 (Glycine max), 3'ss of exon 7
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
gtatatatttatctgctggtcttgttttgaatttgtatgagttgtctcttctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG
|||  ||   || |  |   |||||| |   ||   |  |  |      ||      ||   | ||||||| |   || |      | ||||||||| ||| || ||        | ||||||||||||||||||||||| ||||||||||| |||||||| || |
gtaattaagcat-tcttctacttgttctctgttcacaaaacgtag----tcaaaaatttgcttgtgttgatatcactttc-----ctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG

upper sequence: GLYMA06G13210.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
----------------------------------gtatatatttatctgctggtcttgttttgaatttgtatgagttgtctct-tctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG
                                   ||  |  |  | ||    |    |  ||| ||    ||  || |  |  | | | ||| ||  || |||||||  ||| ||   ||||||||||||||||| ||||||| |   |  |||||||||||||||||||| || ||||||||||| |||||||| ||||
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatg-attttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG

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|17963401|gb|BM270150.1|BM270150
EST:     GTTAGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATG                         CTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
genomic: GTTAGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATGgtatatattt ... attttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
EST: gi|208218386|gb|GE020436.1|GE020436
EST:     GTTAGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATG                         CTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
genomic: GTTAGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATGgtatatattt ... attttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
EST: gi|208104637|gb|GD905020.1|GD905020
EST:     GTTAGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATG                         CTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
genomic: GTTAGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATGgtatatattt ... attttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
EST: gi|208254047|gb|GE052567.1|GE052567
EST:     GGGTTTAGAAGATTCTCGAGTGCATCTGCATGTTGGTGATG                         CTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
genomic: GGGTTT-GAAGATTCTCGAGTGCATCTGCATGTTGGTGATGgtatatattt ... attttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
EST: gi|193561796|gb|FK521701.1|FK521701
EST:     GGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATG                         CTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
genomic: GGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATGgtatatattt ... attttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
EST: gi|208328485|gb|GE127557.1|GE127557
EST:     AGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATG                         CTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG
genomic: AGCTGTTGGGTTTGAAGATTCTCGAGTGCATCTGCATGTTGGTGATGgtatatattt ... attttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgtctcttctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG
                         tgttgat  putative branch site (score: 4)
                               ttttttttccacccat  CT-rich tract
                  tttagtttgttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatatttatctgctggtcttgttttgaatttgtatgagttgtctcttctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG