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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctattattgtaatcacgtttctggtagaagctttatatatgttaattataaatttgctgacatttactttactgaaatgtaaatactatgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAACACCCAGACTTCCACATTACCTCTTCGACCATTCTTGCATCAACGTTAC

Basic information

species Glycine max
transcript GLYMA08G19970.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv12s0034g02140.t01 (Vitis vinifera), 3'ss of exon 13
ttctattattgtaatcacgtttctggtagaagctttatatatgtt--aattataaatttgctgacatttactttac-tgaaatgtaaatactatgtta--ttaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAACACCCAGACTTCCACATTACCTCTTCGACCATTCTTGCATCAACGTTAC
    | ||||     |||    || ||  |   | | |    |||  ||||     | |||| | | ||  | |   | | ||   |||  |   ||   || |||| || || || ||| |||  |||||||||||||| || |||||||| | |||||||||||||||||||||||| || ||||| ||||| || ||  |||
----aatatttgtggcacaac-ctagtctagtttgtgtcagcgttggaatttggtttatgctaaaaattgatctctatcatatcccaatgttgcattcgtttcagGTCCCTGCTCTACAACGGTTTATGCAAAATCGACGTTCGCAACTTCAGCCACACCCAGACTTCCACATTACCTCCTCCACCATCCTTGCCTCGACTCTAC
















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|57575248|gb|CX548223.1|CX548223
EST:     CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAG                         GTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
genomic: CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAGgtaatgagtg ... tgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
EST: gi|208220784|gb|GE018522.1|GE018522
EST:     CACCTTATCCTGTACTTTTGGAATCGGTTTGAG                         GTACCGGCACTGCAAAGGCACATGCAAAATCGACGGTCACAACTTCAACAA
genomic: CACCTTATCCTGTACTTTTGGAATCGGTTTGAGgtaatgagtg ... tgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
EST: gi|254330529|gb|GR841794.1|GR841794
EST:     ATCCTGTACTTTTGGAATCGG-TTGAG                         GTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
genomic: ATCCTGTACTTTTGGAATCGGTTTGAGgtaatgagtg ... tgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
EST: gi|7589379|gb|AW705154.1|AW705154
EST:     CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAG                         GTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
genomic: CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAGgtaatgagtg ... tgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
EST: gi|5606329|gb|AI900427.1|AI900427
EST:     CTGCAGCTNTTATGCAACACCTTATCCTGTACTNTTGGAATCGGNTTGAG                         GTACCGGCACTGCANAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
genomic: CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAGgtaatgagtg ... tgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
EST: gi|58023297|gb|CX710038.1|CX710038
EST:     CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAG                         GTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA
genomic: CTGCAGCTTTTATGCAACACCTTATCCTGTACTTTTGGAATCGGTTTGAGgtaatgagtg ... tgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattataaatttgctgacatttactttactgaaatgtaaatactatgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAACACCCAGACTTCCACATTACCTCTTCGACCATTCTTGCATCAACGTTAC
           tgctgac  putative branch site (score: 2)
                               aaatgtaaatactatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctattattgtaatcacgtttctggtagaagctttatatatgttaattataaatttgctgacatttactttactgaaatgtaaatactatgttattaagGTACCGGCACTGCAAAGGTACATGCAAAATCGACGGTCACAACTTCAACAACACCCAGACTTCCACATTACCTCTTCGACCATTCTTGCATCAACGTTAC

- - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgac