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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgatatatgttcacttgccagattcttgagtgtttcaaattttcaatgacaatcgtgttatctttttaatatatgtttttctatgacatccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGTAGCTGAAGTTCTTGAGAGGAACAAATTACCTGGTGCAATATTCACCTCT

Basic information

species Glycine max
transcript GLYMA15G19670.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G54100.1 (Arabidopsis thaliana), 3'ss of exon 8
-tgtgatatatgttcacttgccag-attcttgagtgtttcaaattttcaatgacaatcgtgttatctttttaatatatgtttttctatgacatccatt--aaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGTAGCTGAAGTTCTTGAGAGGAACAAATTACCTGGTGCAATATTCACCTCT
 | | ||| ||  | ||     |  | ||||||    |  ||||||  | ||    | |  |  | |   |||||  |  |     ||       |||  | ||||| ||||||||||| || || || |||||||| ||  |||| |||||||||||||||||| | ||||  ||||| ||||| ||||| || || ||  | 
gtttcata-atagtaacacaatattaatcttga-caatgaaaatttgtattggt--ttgattggtgtagctaatacttaatacatcatacatgtgattccacagGAAAGGTGCTCCAACTACACCGTTAATAACTATCGCAATGACCAAGCTAGTAGCTGAAGTTTTAGAGAAAAACAACTTACCCGGTGCCATTTTTACGGCC

upper sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 7
-tgtgatatatgttcacttgccagattcttgagtgtttcaaattttcaatgacaatcgtgttatctttttaatatatgtttttctatgacatccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGTAGCTGAAGTTCTTGAGAGGAACAAATTACCTGGTGCAATATTCACCTCT
 |||  | | | | |  || | | |     ||    |     ||         |   || ||||  |   ||   |    || | || || | ||||| |||||||||||||||||||||||  |  | || ||||| |||||||||||||| ||||||||||||||||  ||||| || || ||||||||||||||||||
ttgttctctttatcctttt-ctataagaaggaagactcttgtttccttgaattacatgttttatgctagaaaatgactacttaccataacctacattatagGAAGGGTGCTCCAACAACTCCACTAGTCACCATTGCCGTGACAAAGCTAGTGGCTGAAGTTCTTGAGAAAAACAACTTGCCAGGTGCAATATTCACCTCT
















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|192311334|gb|FK003791.1|FK003791
EST:     GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAG
genomic: GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAA-GGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAG
EST: gi|254315873|gb|GR825682.1|GR825682
EST:     GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAA-GCTAGT
genomic: GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
EST: gi|254334456|gb|GR844241.1|GR844241
EST:     CTAGGATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
genomic: CTAGGATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
EST: gi|192309267|gb|FG999144.1|FG999144
EST:     TGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTTGT
genomic: TGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
EST: gi|192311335|gb|FK003792.1|FK003792
EST:     GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
genomic: GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
EST: gi|151412062|gb|EV281874.1|EV281874
EST:     GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
genomic: GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
EST: gi|27446368|gb|CA953491.1|CA953491
EST:     GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
genomic: GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT
EST: gi|254317668|gb|GR826652.1|GR826652
EST:     GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTG                         GAAGG-TGCTCCAACAACTCCTTTGATA-CTATTGCTGTGACAAAGCTAGT
genomic: GATGGAATGCTTGCATTGCTTTAGTCTGTGGTAACTGTGTTGTGTGgtatgtctat ... tccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgacaatcgtgttatctttttaatatatgtttttctatgacatccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGTAGCTGAAGTTCTTGAGAGGAACAAATTACCTGGTGCAATATTCACCTCT
                    ttttaat  putative branch site (score: 3)
            tgttatctttttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgatatatgttcacttgccagattcttgagtgtttcaaattttcaatgacaatcgtgttatctttttaatatatgtttttctatgacatccattaaagGAAGGGTGCTCCAACAACTCCTTTGATAACTATTGCTGTGACAAAGCTAGTAGCTGAAGTTCTTGAGAGGAACAAATTACCTGGTGCAATATTCACCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - -cacttgc
- - - - - - - - - - - - - - tgagtgt
- - - - - - - - - - - - - - - - - - - - - - -caatgac