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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcactctctttctatttttcttacttctgtttttattttcatcccattctctctcatcgctctcttccgcgattgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG

Basic information

species Glycine max
transcript GLYMA13G39120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G39120.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G131120_T01 (Zea mays), 3'ss of exon 1
-----------gttcactctctttctattt-ttcttacttctgtttttattttcatcccattctctctcatcgctctcttccgcgattgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
           |||| | |   ||||      |||    ||   |   |  |  |||  || |    |      |    || ||    ||| ||||||||||||||||||| ||||| || || ||||| ||||||||
gtgagccagcggttctcccctcttctgcccgctctgtgatcccatccgacctcgatctaatgcggggtttgtttttctctctgcttgcgctgtgcagAGCCGCAAGGACGTGGAAGGGTCGCTGTTCGTCGTCAAGAG
















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|213595694|gb|DB962466.1|DB962466
EST:     CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGG                         AGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
genomic: CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgttcactctc ... tgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
EST: gi|213593287|gb|DB969917.1|DB969917
EST:     CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGG                         AGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
genomic: CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgttcactctc ... tgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
EST: gi|209709701|gb|BW673969.1|BW673969
EST:     CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGG                         AGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
genomic: CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgttcactctc ... tgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
EST: gi|151408519|gb|EV278327.1|EV278327
EST:     CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGG                         AGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
genomic: CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgttcactctc ... tgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
EST: gi|9819945|gb|BE555458.1|BE555458
EST:     CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGG                         AGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
genomic: CCGCCGCACATGTCACCTTCTACGAGTTCAACATCGACCTCAGTCAATGGgttcactctc ... tgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttattttcatcccattctctctcatcgctctcttccgcgattgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG
                                            ttgcttt  CT-rich tract
     tattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcactctctttctatttttcttacttctgtttttattttcatcccattctctctcatcgctctcttccgcgattgctttgcagAGCCGCAAGGACGTTGAAGGATCTCTCTTCGTTGTCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG