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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcacctaatcaactacatctaagatttgctcttgcctaattttgttttactaatgtgagtgatgatgtggtctgtgtttgtggggttgggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTGATGAAGAAGTTTTTGCTGATAACACGGACAGATTTTCTAGCATCTCCAC

Basic information

species Glycine max
transcript GLYMA16G24570.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G24570.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g02610.t01 (Vitis vinifera), 3'ss of exon 2
aaagcacctaatcaactacatctaagatttgctcttgcctaattttgttttactaatgtgagtgatgatgtggtctgtgtttgtggggttgg---gtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTGATGAAGAAGTTTTTGCTGATAACACGGACAGATTTTCTAGCATCTCCAC
                           ||| || |       | |   |  |||  ||||| ||   |||  ||     | | |||| |||    ||    ||||||| || |||||||||||||| ||||| |||||||||||| || ||||||||||||||||  | ||||| |    ||||||| | |||  | |||| |
--------------------------gtttcctttctgtccctctccatacactcttgtga-tgcatatgcagtacacttatatgggattgttctgtcgatagGAACCGGGAAGAGCAGAGAGGGCATTTGCAAGATATGATTATCTGGCAGTGATGAAGAAGTTCCTCCTGATCAACAAGACAGATCTACTAATAGCTCCGC
















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|192333317|gb|FK024294.1|FK024294
EST:     AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
genomic: AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
EST: gi|16996055|gb|BM085427.1|BM085427
EST:     AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAACCTGGTAGAGCAGAGAGGGCTTTTGCT
genomic: AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCT
EST: gi|254336912|gb|GR843091.1|GR843091
EST:     AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
genomic: AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
EST: gi|254336913|gb|GR843092.1|GR843092
EST:     AACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAA-CTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
genomic: AACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
EST: gi|151393066|gb|EV262941.1|EV262941
EST:     AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
genomic: AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
EST: gi|192333316|gb|FK024293.1|FK024293
EST:     AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
genomic: AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
EST: gi|51341471|gb|CO982788.1|CO982788
EST:     AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAG                         GAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG
genomic: AAACTATCAGGAAATTAATTGGAGATGAGAGTCATGTTTGCCAGTTCCAGgttccttgta ... gggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttactaatgtgagtgatgatgtggtctgtgtttgtggggttgggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTGATGAAGAAGTTTTTGCTGATAACACGGACAGATTTTCTAGCATCTCCAC
     tactaat  putative branch site (score: 1)
     tactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagcacctaatcaactacatctaagatttgctcttgcctaattttgttttactaatgtgagtgatgatgtggtctgtgtttgtggggttgggtgtgcagGAACCTGGTAGAGCAGAGAGGGCTTTTGCTAGATATGATTATTTGACAGTGATGAAGAAGTTTTTGCTGATAACACGGACAGATTTTCTAGCATCTCCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - cacctaa
- - - - - - caactac
- - - - - - - - - - - - - - - -ctcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggg