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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttacttctaatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaatttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG

Basic information

species Glycine max
transcript GLYMA08G20020.1
intron # 35
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 15
tttacttctaatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaatttgcattcaatg-------gttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG
        |  ||| |    ||  |   ||  || |    | |       |    | |        | || |  |   |   || | | |||          |||||||||| || |||||||||||||||| ||| ||||| |||||||| || ||||||||||| |||||||| || |||||||| ||||| |||||  |||  |
-----acatgctgtggtg--tgcagagattaatggaagaaactacacaaatgcagtttacagatgtgaacatgtgtgaatgcttacttgcaacacctttatattcagGATCTCCCAAATTATGCTCAGCATACTGTGCCCATATTCTCTCTCCCTCAAGAATGGCTATGGTGTGAATCTTGGTGTGGAAATGCCACAAAGGCAAGAG

upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
lower sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
tttac-ttctaatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaatttgcattcaatggt--tcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG
   || ||  ||  |      | ||     || |  || | |  |  || ||| | | |   | || |   |   ||| |  || | |  || |  |  ||||||||| || |||||||| || ||||  || || || |||||||| || ||||||||||| |||||||| || |||||||| ||||| |||||| |||  |
--gacatttgaagattctgttttttttttctgtttcatgttacataattatttctgtataaatggatgttgcaatgcttac-ttggaacacattaatattcagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG

upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 35
-----------------------------------------------------------------------tttacttctaatg-tagcacctgttgcccttggtgtatatcatttttttttttttttgttttttga---cggacct-tagctgaaatttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG
                                                                       |||| ||  || | |    | | |  | |||    || | |||  | |   | ||| |  ||       |  || | | | ||  || |   |    || |||||||||||||||||||||||||||||| |||||| || || || || || ||||| ||| | |||||||| || |||||||| || || |||||| | ||||
gcaagttgtataatatggttctctatacttagggctgtaacctttctttggtggtcacactatcgttttactttatttgaaaggcttttgcatttgactcttaccatacaccatgctctgaatctttagagttccaggttcaaacatattgatggcatgtcattattttgtttcagGATCTTCCTAATTATGCTCAGCATACTGTTCCTATATTTTCACTTCCCCAAGAGTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGG

upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
lower sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
tttacttct-aatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaat--ttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG
   || ||| ||||   || |  ||   |||  | | | ||  |||  ||  || || ||||   |   |  |    ||   |  | ||  || |   ||||||||||||| || | |||||||||||  || ||||| || || || || ||||| ||| | |||||||| |||||||| || |||||||||||||| ||||
--aacatctgaatgctccatcattttatctttttatgt-tctgtttgcttgattattattttccaaataatatgcattgctctgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG

upper sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
lower sequence: PP1S25_65V6.1 (Physcomitrella patens), 3'ss of exon 17
----------------------------------------------------------------tttact--tctaatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaatttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG
                                                                || | |  || ||    |  |   |||  ||    || |             | ||   || ||  |     | || |||| |  | |||     | | |||||  | || ||||| || |||||    || || || || ||  | || ||| |||||||||||||||||||||||||||| || || || || ||  |||
gttagttagaatagtacattaacgagaatgttttggccagactacggaatgcatgtacagccctttgaatactccaactctgttcaatttgagctcccagtctcctgaagcaaccgtcttactttattccatcacacgtaactgacaact-catctg--gatacagGACTTGCCAAATTACGCCCAGCACCAAGTGCCAATCTTTTCCTTACCCCAACAATGGCTTTGGTGTGAGTCATGGTGTGGGAACGCAACCAAGTCTCAGG

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|15204868|gb|BI427636.1|BI427636
EST:     TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
genomic: TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgttagaggtt ... aatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
EST: gi|33389227|gb|CA852434.1|CA852434
EST:     TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTAT
genomic: TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgttagaggtt ... aatggttcagGATCTTCCTAATTAT
EST: gi|112361150|gb|EE400121.1|EE400121
EST:     TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
genomic: TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgttagaggtt ... aatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
EST: gi|22523540|gb|BU082360.1|BU082360
EST:     TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
genomic: TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgttagaggtt ... aatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
EST: gi|20812577|gb|BQ297055.1|BQ297055
EST:     TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
genomic: TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgttagaggtt ... aatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
EST: gi|12690009|gb|BG156345.1|BG156345
EST:     TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAG                         GATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA
genomic: TCTATGAAACCCTTAGCAAGGATCCAAATAGTCTAGCCAACTTGGATCAGgttagaggtt ... aatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttttgttttttgacggaccttagctgaaatttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG
              ttttgac  putative branch site (score: 3)
     ttttttgttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttacttctaatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaatttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG

- - - - -aatgtag
- - - - - - - - cacctgt
- - - - - - - - - - - -tgccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattc