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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC

Basic information

species Glycine max
transcript GLYMA06G11920.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g41780.1 (Oryza sativa), 3'ss of exon 7
---gatggatgaacaaggtttaatt-taaggcgtaaatctaagctttatcttc------ttgatacatttcttg----gtcagttaatcccattgcatggat------ttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
     |  ||  | |   ||| |     | | | || |||    ||| | ||       | ||||    | | |    |||     |   |||      |||      || |  |  |||||||||||| |||||||||||| ||||||| || |||||||||||||| || || || || || ||||| ||||||||||| ||||||||  | ||||||
gtatttacatacatatattttcacagccatgtggaattcttttttttttttttagaaaatggatagccatgtggaaatgtcttcagaaatcatcatgctgatgctatgttcatttcccagCTTGGTGAAGTTCTTGACACCTTCATCTGGGCTTCAAGGATACTGGGATCCATACCCGATCGACATGGAATTTCGACCACCATGCATGGTGTTGTCAACC

upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os10g41760.1 (Oryza sativa), 3'ss of exon 7
gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
  |   |  | |    | || | | | |    | ||   | ||      ||   |||  || |  |  | | || | ||   ||  || |    |  |||||||||||| |||||||||||||||||||| || ||||| |||||||| || || || || || |||||||||||||| || ||||||||  | ||||||
-gtatttacatacatatcaactaaggac----aactggccattgaaaatttttcacaaatcatcat--gctgatgctat---attcatct---ttgtcagCTTGGTGAAGTTCTTGACACCTGCATCTGGGCTCCAAGGGTACTGGGATCCTTACCCCATCGACATGGAGTTTCGACCGCCATGCATGGTCTTGTCAACC

upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G171390_T04 (Zea mays), 3'ss of exon 6
gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
   | ||| |    || |   |  | |  |  || || | | | | | | |   | |   |||  ||| ||  ||     || ||  | ||  | | ||| ||||| || ||| ||||||| || ||||| || ||||| ||||||||||| || || || || |||||||| || ||||| |||||||| ||||| |||
---gtatgtat---gtatgtatgtatgtatgtatgtatg-tatgtataccttccataccacttcttcaattcgtcaggaagc-tgactgtgttccttcagTTTGGTCAAGTTCCTGACACCCGCGTCTGGGCTCCAAGGGTACTGGGACCCGTACCCGATCGACATGGAGTTCCGGCCACCGTGCATGGTCCTATCGACC

upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G44446.2 (Arabidopsis thaliana), 3'ss of exon 7
gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
              ||||  |||||  |  |    ||  || |    |  | | |     ||||||   |||| |    ||      ||||    ||||| |||||||| || || |||||| | || || || |||||||||||||| || |||||||| |||||||| |||  |||||| || || ||| |||| || 
--------------gtttcttttaactctca---ttactctgttcagtgctaagatgaaacttggt---ttaagctttctgtt----tttggtactgcagTTTGGTGAAGTTTTTAACACCTACCTCGGGTCTCCAAGGATACTGGGATCCATATCCAATCGATATGGAATTTAAACCACCGTGTATTGTTTTATCGACA

upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 3'ss of exon 6
gatggatgaacaaggtttaatttaaggcgtaaat-ctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
              ||||  |       || |||  |    || ||  |  |  |  |   |     ||| | |     ||| ||  || |||| |  ||||||||| ||||||||||||||||||||||| || |||||||||||||| ||||| || || |||||||| |||||||||||||| ||||| || ||||||
--------------gtttgttcc----tgtcaatattgcatttcatggttattttggagggcccatccagcttaagtt-ttgtatt-atctgaattctcagCTTGGTAAAATTCTTGACACCTGCATCTGGACTCCAAGGATACTGGGATCCCTACCCCATAGATATGGAATTTCGACCACCTTGTATGGTGCTGTCAACC

upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ15257 (Selaginella moellendorffii), 3'ss of exon 6
gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
                                                 ||  |  ||   ||||||  ||        |  |    |       | |||||  ||||| |||   ||||||| |      ||||  || |||||||| || ||||| ||||||||||||||| | | ||| ||||||||||| || || 
------------------------------------------------gttcgtttatcg-ttggtctcttttcgtgtcttaacaattccttggctccagCTCCGTGAAGTTCCAAACACCTGTAGAGACTCTACGTGGCTACTGGGATCCATATCCCATTGATATGGAGTTTAGGCGACCGTGCATGGTTCTCTCGACG

upper sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ08372 (Selaginella moellendorffii), 3'ss of exon 6
gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
                                      | |   |  || |  | | | | || ||   ||||  | ||| | ||| |         |||||  ||||| |||   ||||||| |      || |  || |||||||| || ||||| ||||||||||||||| | | ||| ||||||||||| || || 
--------------------------------------gttcgtttatcgttcttc-tcttttcgtgtcttaa--ctattccttggctc--------cagCTCCGTGAAGTTCAAAACACCTGTAGAGACTCTGCGTGGCTACTGGGATCCATATCCCATTGATATGGAGTTTAGGCGACCGTGCATGGTTCTCTCGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC
                      agttaat  putative branch site (score: 4)
       atacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatggatgaacaaggtttaatttaaggcgtaaatctaagctttatcttcttgatacatttcttggtcagttaatcccattgcatggatttgaacttgcagCTTGGTGAAATTCTTGACACCTGCATCTGGCCTACAAGGATACTGGGACCCCTATCCAATTGATATGGAGTTTCGACCACCTTGCATGGTTCTATCAACC

- tggatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgga