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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttatattatcacaatatcacttcattatttatttggtttgtttatttgttagtaattgtctacattttgaaattcttgagttggtaattctttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATTGGACGTGCAGCGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA

Basic information

species Glycine max
transcript GLYMA12G31980.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G32430.1 (Arabidopsis thaliana), 3'ss of exon 10
-----------------------------------------------------------------------------------ctttttatattatcacaatatcacttcattattta---tttggtttgtttatttgttagtaattgtctacattttgaaattc-ttgagt-tggtaattc-----tttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATTGGACGTGCAGCGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA
                                                                                   || |  |  | |  | ||| |   ||  | |   |    ||     |   || ||   |||| ||   |   | ||| || |  | | | || |  ||      || |||||||||||||||| ||||| ||||||||  | ||||| |||||||| || |||||||| ||||| || ||||| || |||||  |||| |||||||||||
gtaccttccttcaaatatctatagactcagttcaatacatcttagatgattgtgaagtggtaaaaggttaaacttagttagttctatgcacctaactagaatgtttttttttaaaacaaaccttaaccag--aatctggatgtaaatggtaatcatatgatatacactaaatatgattcttggtgaattgcagATTGTGAATGGAAGGCACAAGCAGGCAACATATGTGTAGCTTCATTCGACTGGACGTGTAGCGGTATCTGCAGATCAGCTGATCGGATAAAAGAGGTTCA

upper sequence: GLYMA12G31980.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0059g00640.t01 (Vitis vinifera), 3'ss of exon 10
ctttttatattatcacaatatcacttcattatttatt-tggtttgtttat--ttgttagtaattgtctacattttgaaattcttgagttgg--taattctttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATTGGACGTGCAGCGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA
      |  |   ||   |||        | |  ||       |||| |      | |  |||| |  |||| |   || | || | |     |  ||  | |||||||||| ||||| || |||||||||||||  ||||||||||||||||||||||  ||||| ||||||||||||||  |||| ||||| || ||||| ||
-----cacgtgtacaagctatgggaaagatttgcatgacaagctgttgacaacaatcaacaattatacacatctgtgaaattttaattgaaacttgttactgcagATTGTGAGTGGAAGGCCCAGGCAGGCAATGCATGTGTTGCTTCATTTGATTGGAGCTGCAGTGGAATTTGCAGGTCATCTGAGAGGATTAAGGAGGTCCA
















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|208051629|gb|GD852508.1|GD852508
EST:     GATCGAAGACTCTGCTGTGGTACACCACCAG                         ATTGTGAATGGAAAGCACAGGCGGGCAATGTTTGTGTTGCTTCATTTGATT
genomic: GATCGAAGACTCTGCTGTGGTACACCACCAGgtgaaggttt ... attctttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATT
EST: gi|20498515|gb|BQ273445.1|BQ273445
EST:     AGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGTACACCACCAG                         ATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTTGT-GCTTCATTTGAT
genomic: AGATGTGGACCACATAGATGATCGAAGACTCTGCTGTGGTACACCACCAGgtgaaggttt ... attctttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGT-GTTGCTTCATTTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgttagtaattgtctacattttgaaattcttgagttggtaattctttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATTGGACGTGCAGCGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA
                                              ttctttc  CT-rich tract
                   tacattttgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttatattatcacaatatcacttcattatttatttggtttgtttatttgttagtaattgtctacattttgaaattcttgagttggtaattctttcagATTGTGAATGGAAAGCACAGGCAGGCAATGTTTGTGTTGCTTCATTTGATTGGACGTGCAGCGGAATTTGCAGGTCTGCTGAAAGGATCAAAGAGGTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - -cacttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggta