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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagtttcataactttgctattaccttctagaaattcagagtatgccatgatcaatgagttaatgaaaattaatgttatacctctaatttgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCTGAAA

Basic information

species Glycine max
transcript GLYMA07G40060.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40060.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0568g00010.t01 (Vitis vinifera), 3'ss of exon 4
gagtttcataactttgctatta-----ccttctagaaat-tcagagtatgcca-tgatcaatgag-ttaatgaaaattaatgttatacctctaatttgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCTGAAA
   ||   |  ||    |||||        | | || || ||| | | ||  | | | || |  |  |  |||  |||| ||||     |   ||| ||   |||||||||||||||||||||||| | ||||||||||||||||| || ||| | ||   ||  || || || || ||||| || |||| || |||||   ||||| 
---ttcttttcctgcaatattagggaatgatttggatatatcaaaatgtgtaaataaccattctgacttctgagtattattgtt-----tggtattggtgtattgcagTTGAGGAACTTGGTTTGGTCTACATCAAAGCATGATGTCTACCTTATGTCTCATTTTTCTATCATTCATTGGTCTTCGTTAAGTTGCAAGAAGACTGAAG
















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|151396369|gb|EV266246.1|EV266246
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAACATGATGTATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtacgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCG
EST: gi|192324872|gb|FK015368.1|FK015368
EST:     ATTTCTGGCAAAACACTCAATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGACAACATCAAAGCATGATGTATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtacgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCG
EST: gi|19345980|gb|BM890860.1|BM890860
EST:     ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCG
genomic: ATTTCTGGCAAAACACTCGATCTGTGAAATCAACAATACTTCATTTCCAAgtacgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCG
EST: gi|193400537|gb|FK369690.1|FK369690
EST:     TGAAATCAACAATACTTCATTTCCAA                         TTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCG
genomic: TGAAATCAACAATACTTCATTTCCAAgtacgttagt ... tcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatcaatgagttaatgaaaattaatgttatacctctaatttgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCTGAAA
                                   ctctaat  putative branch site (score: 3)
       aatgagttaatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagtttcataactttgctattaccttctagaaattcagagtatgccatgatcaatgagttaatgaaaattaatgttatacctctaatttgtcatttgcagTTGAGGAACTTGGTTTGGGCAACATCAAAGCATGATGTATATCTTGTTTCGAGTTACTCAATTATACACTGGTCGTCTTTAAATTCCAAGAGATCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC