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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaatgggttgtttaattgtagtagtttgtttgtcaataattcaatgtctttctgttttggatgactatttattgttcagatgttgagctttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC

Basic information

species Glycine max
transcript GLYMA17G01260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
aaaaatg-ggttgtttaattgtagtagtttgtttgtcaataattcaatgtctttctgttttggatgactatttattgttca-gatgttgagctttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC
  | |||  ||||||| ||||  | |      || ||||    | | |    ||||| | |  ||  |   |||    ||  | | |   | ||| | |||||||||| || |||||||| || || ||||| |||||| |  | || |||||||||||||| ||||| ||||||||||||||||| |||||||||||||  
--atatgtagttgtttgattgatgcatagaacttttcaaattgttattagtattctggtctaaatttcggattaaaactctcggtttcttgatttcaatcagGCAACAACAGAGTGATGAGACCCCAATGGTGTGGGAGATACTTCTATACATGTACATCCTTTACTCACCAGATTGGCATTACCGAAGTACAATGCCCACT

upper sequence: GLYMA17G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S70_225V6.3 (Physcomitrella patens), 3'ss of exon 2
aaaaatgggttgtttaatt-gtagtagtttgtttgtcaataattcaatgtctttctgttttggatgactatttattgttcagatgttgagctttaatt---cagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC
    || | |  |  |    ||   |  |||| | |    | ||| |||   ||||        || |  ||   ||| ||  ||   | |||| |     ||| ||||||||||| ||||| || |||||||||||||   || | || ||||| ||  | || |||||||| ||||||||||| ||||||||||||||||  
---tattgatcatgcagcaagttacatattgtat-ttggaagttctatgagattcttacacacttgtcatttggctgtgcatgtgaccaacttttaacgagcagTCAACAGCAAAGCGATGAGACGCCTATGGTATGGGCAATGCTTCTTTACATCTATGTACTTTACTCTCCCGATTGGCATTATCGCAGTACAATGCCCACT

upper sequence: GLYMA17G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S452_16V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------aaaaatgggttgtttaattgtagtagtttgtttgtcaa--taattcaatgtctttct-------gttttggatgacta-----tttattgttcagatgttgagctttaatt--cagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC
                                                                       ||   || |    |    || |   |||  |   ||  || |||||||||   ||       || |||  |||| |     |||||||||   ||||    || |      ||| ||||||||||||||||| |||||||||||||||| | || | || ||||| ||| | ||||||||||||||||||||||| || ||||||||||| |  
gtaagatcttacatcttgctgtttagcagtttttaaccctctactactcgtccataaacgtcgatcttgtgaatctggataagaagggctaatgtcttggcttcaaaattatttcaatgtcacacttacgagcgtattgcctgaccagttcctttattgtttgcatgtgcgactcttgcgagcagTCAACAGCAAAGTGATGAGACTCCTATGGTATGGGTGATGCTTCTCTACATCTACGTGCTCTACTCTCCAGATTGGCATTATCGGAGTACAATGCCTACT

upper sequence: GLYMA17G01260.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S55_117V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------aaaaatgggttgtttaattgtagtagtttgtttgtcaataattcaatgtctttctgttttggatgactatttattgttcagatgttgagctttaatt--cagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC
                                                                                    || || | |  ||| | || | || || |    |  |||     | ||  |  ||| ||   |   || || || ||   |||     | ||      ||| |||||||| |||||||| |||||||||||||||| | || | || ||||| ||| | || || |||||||| ||||| || || || ||||||||||  
gtaagctttttacactttacttttaacagtgctcatatacatcttactcgtccatgcctgtgcttaatgtggacatgcatatcgaatatcgatgttttgactg-aatatttggaagatatataccctcaagttgtagtgtcttac-tagttactttttttttgcatgcgcgacgtttgcgagcagTCAACAGCAGAGTGATGAGACTCCTATGGTATGGGTGATGCTTCTCTACATCTACGTGCTTTATTCTCCAGACTGGCACTATCGGAGCACAATGCCCACA

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|9899574|gb|BE608542.1|BE608542
EST:     ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGT                         GCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
genomic: ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGTgtaagtatct ... tttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
EST: gi|192301965|gb|FG995135.1|FG995135
EST:     ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGT                         GCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
genomic: ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGTgtaagtatct ... tttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
EST: gi|7685216|gb|AW755864.1|AW755864
EST:     ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGT                         GCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
genomic: ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGTgtaagtatct ... tttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
EST: gi|151393200|gb|EV263075.1|EV263075
EST:     ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGT                         GCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT
genomic: ATGACACTTGCCATTGGAAGCATGTTGTACCATGCCACGCTGCAACATGTgtaagtatct ... tttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtctttctgttttggatgactatttattgttcagatgttgagctttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC
                                            ctttaat  putative branch site (score: 4)
                      tatttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaatgggttgtttaattgtagtagtttgtttgtcaataattcaatgtctttctgttttggatgactatttattgttcagatgttgagctttaattcagGCAACAGCAAAGTGATGAAACTCCTATGGTATGGGAGGTGTTGCTGTACATGTACATCCTCTACTCTCCAGATTGGCATTACCGCAGTACAATGCCCATC

- - -tgggttg
- - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgttg