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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttctctctctgtatattttatatatattactgatatttgatatttttatttttaaaaaatttactttttttttttattattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCTACTCACCCACTGGAGTT

Basic information

species Glycine max
transcript GLYMA13G05130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G05130.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G150616_T01 (Zea mays), 3'ss of exon 1
------------------------gttctctctctgtatattttatatata--ttactgatatttgatatttttatttttaaaaaatttactttttttttttattattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCTACTCACCCACTGGAGTT
                         |||   |||||   ||  |   |  |  |  ||| | | |  | || |  |  ||     |||    ||  ||   | ||   | |||||| || | |||||||||||| | |||||| ||||||||| ||||||||||| |  ||| ||| || 
gtgggtatccgtcctaaggattcctttcaagctctggggatcatgggtgcagttcgctggtttattctcttctgttggtttgcttattgttgttggttcgctttttccgcagATCTGCTGTACAAGGACTACCAGACTGACCACAAGTTCACCCTCACTACCTACACCTCCAATGGCGTC
















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|298196194|gb|HO044585.1|HO044585
EST:     CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAG                         ATCTCCTCTTCAAGGACTACCACAGTGGCCAGAAGTTCACCATCACTACCT
genomic: CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAGgttctctctc ... attattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
EST: gi|22525930|gb|BU084741.1|BU084741
EST:     CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAG                         ATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
genomic: CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAGgttctctctc ... attattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
EST: gi|308097870|gb|HO761041.1|HO761041
EST:     CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAG                         ATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
genomic: CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAGgttctctctc ... attattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
EST: gi|209719493|gb|BW669156.1|BW669156
EST:     CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAG                         ATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
genomic: CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAGgttctctctc ... attattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
EST: gi|12773110|gb|BG238037.1|BG238037
EST:     CATGTCGAAGGGTTCTGGTCTCTACTGTGACATTGGCAAGAAAGCCCGAG                         ATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT
genomic: CATGTCAAAGGGTCCTGGTCTCTACTCTGACATTGGCAAGAAAGCCCGAGgttctctctc ... attattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatttgatatttttatttttaaaaaatttactttttttttttattattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCTACTCACCCACTGGAGTT
                             tttacttttttttttt  CT-rich tract
         atatttttatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttctctctctgtatattttatatatattactgatatttgatatttttatttttaaaaaatttactttttttttttattattgtagATCTCCTCTTCAAGGACTACCACAGTGACCAGAAGTTCACCATCACTACCTACTCACCCACTGGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT