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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttactgcttcggatatataacatgtgaatttttttccttgaataattacattaacaagattatcttgtcatttattattttttcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGAAGGAGAGACGTCTATGATCTTCATCATGCTGTGCTGG

Basic information

species Glycine max
transcript GLYMA18G53100.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G53100.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0006g02480.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtttactgcttcggatatataacatgtgaatttttttccttgaataatt-acattaacaagattatct-tgtcatttattattttttcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGAAGGAGAGACGTCTATGATCTTCATCATGCTGTGCTGG
||| |||| || | | | ||| || | | || | || | | || | | | || || || || ||| | | || | ||| || || | ||||| ||| || ||||| |||| | || |||||||| |||||||||||||||||||| | || |
gtaggtttcttgttatcaa-gtctaa-atactatcctagttgtgtatatctctcatatgaggattctgattgatgagggttttttcatttgtgttatcagTTGTATTCAGTTCTGTTGCCTATAACCATTTTTCTCATCATCTATTTTCGTAGGAGAGATGTCTATGATCTTCATCATGCCATCCTAG
















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|209704416|gb|BW680599.1|BW680599
EST:     ATCTCAAATATCCACTGAAGAGTAATACAGTTCCTGCTTGGGCTATTCCT                         ATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGA
genomic: ATCTCAAATATCCACTGAAGAGTAATACAGTTCCTGCTTGGGCTATTCCTgtaagtttac ... tcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGA
EST: gi|18040504|gb|BM308798.1|BM308798
EST:     ATCTCAAATATCCACTGAAGAGTAATACAGTTCCTGCTTGGGCTATTCCT                         ATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGA
genomic: ATCTCAAATATCCACTGAAGAGTAATACAGTTCCTGCTTGGGCTATTCCTgtaagtttac ... tcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGA
EST: gi|192294776|gb|FG986625.1|FG986625
EST:     ATCTCAAATATCCACTGAAGAGTAATACAGTTCCTGCTTGGGCTATTCCT                         ATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGA
genomic: ATCTCAAATATCCACTGAAGAGTAATACAGTTCCTGCTTGGGCTATTCCTgtaagtttac ... tcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaataattacattaacaagattatcttgtcatttattattttttcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGAAGGAGAGACGTCTATGATCTTCATCATGCTGTGCTGG
           cattaac  putative branch site (score: 2)
 tttattattttttc  putative PPT
 attaacaagattatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttactgcttcggatatataacatgtgaatttttttccttgaataattacattaacaagattatcttgtcatttattattttttcatggttagATATATGCAATTTTATTGCCCATAGTGATCTTTCTTGGTGTCTACATCCGAAGGAGAGACGTCTATGATCTTCATCATGCTGTGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG