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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttgatttattaagcgcttttcgtgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCAGATGGACGAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG

Basic information

species Glycine max
transcript GLYMA14G40480.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G40480.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g17700.1 (Oryza sativa), 3'ss of exon 4
gtaagcttgatttattaagcgcttttcgtgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCAGATGGACGAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
                                                                         | |||  || |  || || | |    || | | |||  | | | ||   || |  ||     | |   ||  |  ||| || | |   || | |   |   || |  |||  || |||||||| ||| |||||||||| |||||||||||||| || |||||     | ||  | |  || ||| |  | ||||| ||| | |
-----------------------------------------------------------------------tggcaag--attgtgtagtgctatcaatttatcttatgatttt-cgtt--ttgttttttcatcatgcgtgtgagttgtttattctcagtgtcatctttgttatagGATCTGAGGGGAATACATTCGGCTCGAGAGTTTGTGTGGTGGTATAATGGACATCCAGACATGTGCAACTTGGCACCTGACTTGCAAAGCACAGATTCTG

upper sequence: GLYMA14G40480.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g03550.t01 (Vitis vinifera), 3'ss of exon 4
---------gtaagcttgatttattaagcgcttttcgtgaatttgctagaatttttgttgtttcattggttttgcctgcggtgt-aagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCAGATGGACGAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
          |||   | || | ||  || ||||   | ||||  | |  | | |||    ||  ||  | |  |  | | | | ||  | ||  |||||| | |     ||| ||||   |     | ||    |  |  | ||   | | |||||  || |||   |||| |||| |    ||| | ||   ||| ||||| ||||||||||| ||||||||||||||||||||||| |||||  |   ||| || || || ||  | ||||||||||||||||
gtacgttttataaaaataatgttttgtgc-ctttgtttaaattatccattagtcttgcatattattttctatcacaagggatttcaaatactgaattaatggtttcaggattt-tgataatttaatttcaaaatgttataagcgtagatgtagtttctgttgtttatgtatttcttttc----cagGATTTTGCAGGAATACACTCAGCTAGAGAATTTGTTTGGTGGTATAATGGGCATCCAGACTGCAAAAACCTGGATCCTGATTTGAAGAGCACTGATACAG

upper sequence: GLYMA14G40480.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S302_37V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaagcttgatttattaagcgcttttcgtgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCAGATGGACGAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
                                                                           |  |  |  | |  ||  | ||| ||| |   | |  ||      |    ||||    ||  | |   ||    |  | ||  |   | ||   |   ||| |  ||  |||  ||||| |||| ||||||||||| |||||||||||||| || || |||  |   ||  |  | ||||| ||  |     | ||||| |
---------------------------------------------------------------------------atactttatccttgtgagcatttgtttagctcttggaatattcgcatcattagtgcctgtagcacaacttgtgctgatattt-tccgcgttgagtctgcagGAGCTGGTAGGCGTACATGCAGCAAGAGAGTTTGTCTGGTGGTATAATGGTCATCCTGATCAAGTCAACTTGCAACCAGATCTTCAATCTTCAGATACTG

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|254341561|gb|GR852698.1|GR852698
EST:     TCCTTGCATATGGTGCCGAAAGTGATAGAAGTCTTGGTATTCCAGGGGAG                         AACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGG
genomic: TCCTTGCATATGGTGCTGAAAGTGATAGAAGTCTTGGTATTCCAGGGGAGgtaagcttga ... tccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGG
EST: gi|23058880|gb|BU578342.1|BU578342
EST:     TCCTTGCATATGGTGCTGAAAGTGATAGAAGTCTTGGTATTCCAGGGGAG                         AACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGG
genomic: TCCTTGCATATGGTGCTGAAAGTGATAGAAGTCTTGGTATTCCAGGGGAGgtaagcttga ... tccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGG
EST: gi|7692675|gb|AW760776.1|AW760776
EST:     TCCTTGCATATGGTGCTGAAAGTGATAGAAGTCTTGGTATTCCAGGGGAG                         AACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGG
genomic: TCCTTGCATATGGTGCTGAAAGTGATAGAAGTCTTGGTATTCCAGGGGAGgtaagcttga ... tccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCAGATGGACGAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG
                               ttttaat  putative branch site (score: 3)
                ctcttgtttcatttct  CT-rich tract
                   ttgtttcatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttgatttattaagcgcttttcgtgaatttgctagaatttttgttgtttcattggttttgcctgcggtgtaagcaatggcttaatgttcttttattttgtgatggctatgcattaactgatagtttgagttactcttgtttcatttcttttaatattcctttccttctcagAACTTGAAAGGGATACATTCAGCTAGAGAGTTTGTTTGGTGGTATAATGGGCACCCAGATGGACGAAATCTTGAGCCAGACCTAAAGAGCACTGATACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA