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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctcctctttcttaagcagtcattggatttggtgatcggttttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG

Basic information

species Glycine max
transcript GLYMA19G17460.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 18
----gtaaatctcctctttcttaagcagtcattgg-atttggtgatcggtt-ttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG
    | |   |||   | ||| ||| || |  |   || | ||  |   || || | ||    |   |  | | |  |   |  |  ||||| |||||||  ||| | || ||||||||| |||| || ||||||||||||||||| |||||  |   ||||||||||||||| ||||||
gtaagcattcctcgcatatctgaaggagactgtactatatagttgtatcttgttgtaataacatctgacaagtttcatgtgttgtgacagAGGACAGAAATGGAACGGGTCTGCTTTGGTCGATCTGGTATACATGGATGGGGCCTTTTTGCGAGAAGAAATATTCAAGAAGGAGAAATG

upper sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 19
gtaaatctcc----tctttcttaagcagtcat-------tggattt----ggtgatcggttttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG
|||||| | |    | | | || |||| | ||       |  | ||    | |   || |||| |  || | ||| |||  | |  ||||  | | ||||| || |||||||| || ||||||||||||||||| || |||||||| ||||||||||||||||| |||  |||||||||||| || |||
gtaaattttcatcatttctgttcagcaattatcctcctatcaacttcttggattgacgatttttttttttttttgtatgcat-tcatacacgactccagAGGACTGAAAATGATAGGGTTTGCTTTGGTAGATCTGGAATACATGGCTGGGGCCTCTTTGCACGACAAGCTATTCAAGAAGGAGATATG

upper sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ34404 (Selaginella moellendorffii), 3'ss of exon 11
gtaaatctcctctttcttaagcagtcattggatttggtgatcggttttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG
                           || ||    ||  |   ||| | |  | | |    ||   ||      |     |||| ||| || ||    |||||||||||||||| ||||||||| ||||||||||| || |||||  | | | | ||  ||||||| || |||
--------------------------gttcgaacacgtc-taaatttccaggatatat-atgtggccgtgcctggtg----cagAAAACTGAGAAAACGAGAGTTTGCTTTGGTAAATCAGGCATCCATGGATGGGGACTGTTTGCGAGGCGATACATCAAAGAAGGAGAGATG

upper sequence: GLYMA19G17460.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ23651 (Selaginella moellendorffii), 3'ss of exon 10
gtaaatctcctctttcttaagcagtcattggatttggtgatcggttttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG
                           || ||    ||  |   ||| | |  | | |    ||   ||      |     |||| ||| || ||    |||||||||||||||| ||||||||| ||||||||||| ||||||||  | | | | ||  ||||||| || |||
--------------------------gttcgaacacgtc-taaatttccaggatatat-atgtggccgtgcctggtg----cagAAAACTGAGAAAACGAGAGTTTGCTTTGGTAAATCAGGCATCCATGGATGGGGACTCTTTGCGAGGCGATACATCAAAGAAGGAGAGATG

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|193309960|gb|FK277944.1|FK277944
EST:     ACAAGCCTCCAGCATTTTCTTCTTTCAGGGAACGCCTTCATCATTTACAG                         AGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGG
genomic: ACAAGCCTCCAGCATTTTCTTCTTTCAGGGAACGCCTTCATCATTTACAGgtaaatctcc ... ataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGG
EST: gi|9204647|gb|BE330871.1|BE330871
EST:     ACAAGCCTCCAGCATTTTCTTCTTTCACGGAACGCCTTCATCATTTACAG                         AGAACAGAAAATGAAAGAGCTTGCTTTGGTAGATCAGGCATACATGGATGG
genomic: ACAAGCCTCCAGCATTTTCTTCTTTCAGGGAACGCCTTCATCATTTACAGgtaaatctcc ... ataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatttggtgatcggttttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG
                 ttctgat  putative branch site (score: 3)
                                   attgttttacataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctcctctttcttaagcagtcattggatttggtgatcggttttctgattgtcttgcatgattgttttacataatttcagAGAACAGAAAATGAAAGAGTTTGCTTTGGTAGATCAGGCATACATGGATGGGGCCTCTTTGCACGTCAAAATATTCAAGAAGGGGAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG