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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcctcttaaagtatatatcgcctatgtcagtttggcaattttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC

Basic information

species Glycine max
transcript GLYMA08G21570.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 13
-gttagttcctcttaaagtatata-tcgcctatgtcagtttggcaattttcaat-tttgttttccgc-------tgactatgatcttggactc----cagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
    ||    ||  |  | | | | | |  | | |     ||   | | |   | ||| || |  ||         |  |    |||| |  |    |||| || |  |||   |||||||| |||||||| |||||||||||||| || || ||||| ||||||||||||| |||||| || || || |||||  ||||
gagaagccattcacagcgcaaacacttgggtgtcttgtaatgtttactgttggtatttattatgagcaagaagccaagaactgacttgaatgcttctcagGAACGCCATATGCACAGCAATCCTACAAAGTAAGTGATTCATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGGTTCTATGTCACTGCCTTGGC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 13
---------gttagttcctcttaaagtatat-atcgcctatgtcagtttggcaatt--ttcaattttgttttccgctgactatgatct--tggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
         | || |   ||     | ||   |  |   || | |||||   || |    | |  |          ||||| || | |  ||  ||||||| ||||| |||   ||||| || |||||||| |||||| |||||||||| || ||||| ||||||||||||| ||||||||| || || ||||| |||||
ggaaaatgagctactcaatccccgggaatcccagaggggatttaagtttccaaactagccctaaataaacaagtaatgactctggttttctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGTGATACATTTCCTTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G158177_T01 (Zea mays), 3'ss of exon 6
------gttagttcctcttaaagtatatatcg---cctatgtcagtttg--gcaattttcaattttgttttc---cgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
       |   | |     |||||     | |   ||  ||    ||||  || |||   |  |   |   |      |||||       ||  ||||||| ||||| |||   ||||| || |||||||| || ||| ||||||| || || ||||| ||||||||||||| ||||||||| || || ||||| |||||
ttttggttctatgctgtccaaagtgggagtggtaacccttgaatatttgttgccattggtatataaataaacaagtaatgactggttctctgttctccagGAACACAATATGCCCAGCAGTCCTACAAAGTAAGCGATACATTTCCCTTCAAATGGATAAACAAAAAGTGGAAGGAGGGCTTCTATGTCACTGCTATGGC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------------gttagttcctcttaaagtatat-atc-----gcctatgt-cagtttggcaattttcaattt---tgttttccgctgact-atgatcttggactcc--agGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
                                                                      | | ||  ||||| | | | | ||       ||| | |   ||||      | |   |||   ||||    | || || | | | ||    ||   ||| ||   |||   |||||| || |||||||| || || || ||||| ||||||||||| || || || ||| | || ||||||||||||||| |||||||
gtattttattggatagtatcctttgatgtatattgaatctattttcagagttgatctcaagggtgtttgatgatttattcttataatttgtcatttggagacctttttgtggttttctggctcttgttttacttgttgcatgatgtctcacggtgtttatttctgtagGAACGTCGTACACGCAGCAGTCTTACAAAGTGAGCGACTCTTTTCCATTTAAGTGGATCAATAAGAAATGGCGAGAAGGCTTTTACGTGACTTCAATGGC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 11
gttagttcctcttaaagtatatatcgcctatgtcagtttggcaattttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
                     ||| | |  ||| |  |||             ||||    |||||||   |   ||   |  |||| ||||  ||   ||| ||||| |||||||| || ||||||||||| || |||||||| ||||||||||||||||| || |||||||||||| | |||||
--------------------gtattgtcgctgtta--ttgatggccactggcattgt----cgctgac-gcgtgtttcccccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

upper sequence: GLYMA08G21570.1 (Glycine max), 3'ss of exon 13
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 11
gttagttcctcttaaagtatatatcgcctatgtcagtttggcaattttcaattttgttttccgctgac-tatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
                     ||| | |  ||| |  |||             |||||    ||||||   ||||      |  |||| ||||  ||   ||| ||||| |||||||| || ||||||||||| || |||||||| ||||||||||||||||| || |||||||||||| | |||||
--------------------gtattgtcgctgtta--ttgatggccactggcattgtt----gctgacgcgtgattccc--ccgcagGGACACCATACACGCAACAATCGTACAAAGTGAGCGATTCATTTCCGTTCAAGTGGATCAACAAAAAGTGGAGGGAAGGGTTTTACGTGACTTCCATGGC

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|254324032|gb|GR840457.1|GR840457
EST:     CGCAATTGCTGGAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGG                         GCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTA
genomic: CGCAATTGCTGGAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGGgttagttcct ... tggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTA
EST: gi|10236055|gb|BE805003.1|BE805003
EST:     CGCAATTGCTGGAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGG                         GCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTA
genomic: CGCAATTGCTGGAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGGgttagttcct ... tggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTA
EST: gi|6069673|gb|AW099299.1|AW099299
EST:     GAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGG                         GCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTA
genomic: GAGCTGTAAACGGTAGCTCGCTAGTAGTAATGTCTAAGGgttagttcct ... tggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagtttggcaattttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC
                              cgctgac  putative branch site (score: 3)
           aattttcaattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcctcttaaagtatatatcgcctatgtcagtttggcaattttcaattttgttttccgctgactatgatcttggactccagGCACACAGTATTTGCAGCAATCATACAAAGTTAGTGATTCATTTCCTTTTAAGTGGATTAACAAAAAGTGGAGGGAGGGCTTTTACGTGACTGCAATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG