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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtcacaaagcattgtaaaaatgaagattgatcagtggttaattgttatccatgctagctttcttttgttagaatttgacaatacttgttttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGCTTGTGCTACCTGATGAATGACATGGCACAAGAAGCACTTGGAGATGCCA

Basic information

species Glycine max
transcript GLYMA11G14240.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G14240.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv06s0004g05810.t01 (Vitis vinifera), 3'ss of exon 9
agtcacaaagcattgtaaaaatgaagattgatcagtggttaattgttatccatg-ctagctttcttttgttagaatttgacaatacttgttttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGCTTGTGCTACCTGATGAATGACATGGCACAAGAAGCACTTGGAGATGCCA
   | | |  ||   |  || ||   ||   | |    ||| ||  |||   || |  || |  |        ||||||      | | ||||||||||||||||| |||||||| |||||||| ||||| ||||||| ||| || || |||||||| ||| |||||||||| ||| |||||||||| || |||||||| |
-aaccctattcaagttccaagtggtcataattgaagccttactttgtataggtggcccgcatgataagaaataaatttgctcgatccttttttgtgtgtagTTCATTGATGGTGGGACCATGGTGTCACCAACTGTGTTTGCAAGACGTTGCTTGTGTTACTTGATGAATGAGATGCCACAAGAAGCTCTAGGAGATGCAA
















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|207751700|gb|GD722615.1|GD722615
EST:     GACTGCTATACACAA                         TTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
genomic: GACTGCTATACACAAgtaagtcagc ... ttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
EST: gi|58019757|gb|CX706499.1|CX706499
EST:     CTGCTTTCCATGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAA                         TTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
genomic: CTGCTTTCCATGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAAgtaagtcagc ... ttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
EST: gi|58022801|gb|CX709542.1|CX709542
EST:     CTGCTTTCCATGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAA                         TTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
genomic: CTGCTTTCCATGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAAgtaagtcagc ... ttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
EST: gi|208185441|gb|GD984223.1|GD984223
EST:     TGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAA                         TTCATCGATGGTGGAACCATGGTATCACCAACCGTGTATGCCAGGCGCTGC
genomic: TGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAAgtaagtcagc ... ttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
EST: gi|22928886|gb|BU546025.1|BU546025
EST:     CTGCTTTCCATGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAA                         TTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC
genomic: CTGCTTTCCATGCTAGAGACTTCTCCACGGCCATTGACTGCTATACACAAgtaagtcagc ... ttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatccatgctagctttcttttgttagaatttgacaatacttgttttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGCTTGTGCTACCTGATGAATGACATGGCACAAGAAGCACTTGGAGATGCCA
                            atttgac  putative branch site (score: 4)
                                       cttgtttt  putative PPT
                  ttttgttagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtcacaaagcattgtaaaaatgaagattgatcagtggttaattgttatccatgctagctttcttttgttagaatttgacaatacttgttttgtgtgtagTTCATCGATGGTGGAACCATGGTATCACCGACTGTGTATGCCAGGCGCTGCTTGTGCTACCTGATGAATGACATGGCACAAGAAGCACTTGGAGATGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - -caaagca
- - - - - - - - - -aatgaag
- - - - - - - - - - - - - - - - -agtggtt
- - - - - - - - - - - - - - - - - - - - - - - - -ccatgct