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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG

Basic information

species Glycine max
transcript GLYMA01G29470.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatct-agatgttaacttat----ttctgtgccttatttattcac-agATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
                |||  | |  ||| ||   ||   | |  | ||| | || |  || | |||| |  |  | |    | || |   || | | ||||| |||||||||||||||| || ||||| ||||| |||||||||||||| |||||| | || || || ||||||||||| ||||| |||| ||| || ||||| |
---------------gtaaactcctcttttttttttggtatatgcaaatg-taatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 10
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttat--tcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
          || ||      || | ||| | |  | || || | |  | ||    |  || | ||| |    ||| || | | ||| || |    |  |||||||| |||||||| || ||||| || || ||||| || ||||| ||||||||||| || |||||||||||||| ||||| ||| |||| |  ||||| |
----gtaaactgtcagctggataacttttttagtttttaattcagaagtactt---cttattt-gatatcttgttactt-tatccctaatatgctatttcagATGGCAGAATATAGGATTTCAATCTACGGAAGGAAACAGAGTGAATGGGACCAACTTGCAAGTTGGATAGTGAACAATGAATTGCACAGTGGAAATGTTG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 10
-ttggacttgttgacaataatttacca-----tttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
  |||  ||| | | |||  | |  ||     | |  |  |   ||   ||  ||  |    |   | |   | ||  || || |||  |  ||    | |  |||||||||||||| |||||||| |||||||| || ||    || |||||||||||||| || |||||||| ||||| |||||| | ||||| |||||||| |
catggcattgctca-aattctgtgtcaagaaatcttcttgccaaagcagatccataattgctctgtttt--gtttttcctgatgtctacg--ttgaacact-gcagATGGCTGAATACAGAATATCTATATATGGCAGAAAAATGAGCGAGTGGGACCAACTCGCTAGTTGGATTGTGAACAATGATCTATACAGTGAGAATGTTG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 10
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgt-taacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
  ||   | || |     || |       |    ||||  || || |||     |    ||   | | | ||| ||  |  ||     |  |     ||||||||||||||| || |||||||||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||| |
-agggaatcttcatctgcatgtgtatgagcccatctgtttttgatttatttgtttatttattatggtttgtaaattcctgatgctaaatgctatgctacagATGGCTGAATACAGGATATCAATATATGGCAGAAAGCAAAGTGAGTGGGACCAACTTGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTG

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------------------------ttggacttgttgacaat---aatttaccatttcttgactgtagtttatatatgctcatccccatctagatg-------------ttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
                                                                         |  | |   || ||||    |    || |  | |||| ||      | | |||    |     | | || |             || | |    ||     | |||| | |  |||||||| || |||||||| || || ||||| |||||| ||||||| ||||||||  ||||||||||||| || | |||  |  |  | || ||||||||  
gtaaacatctacaacttcttttcaattaaatttttttattagatgtttttgtactccattttgaaataccacttctgcccaattcacaaccccaccacacaaggttttgagtgagcaacacacatgggttttgagtttttgaggggcatgaagtccattgaatcccatcaacagcatattcactttcagATGGCAGAGTATAGAATTTCTATCTATGGGAGGAAGGAAAGTGAATGGGACCAGTTAGCCAGTTGGATTGTCACTAACAAACTTCAAAGTGAGAATGTGA

upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
-ttggacttgttgacaataat-ttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
     || |  || | ||  |  ||  | |  ||  || ||      | || ||    |      |||         || | |||   ||  || |    |||||||||| ||||| |||||||| || || |||||| | ||||||||||| ||||| |||  |||||| ||  | ||| |  || |||| ||||| ||| 
tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgt--gtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCA

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|7925052|gb|AW831078.1|AW831078
EST:     GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAG                         ATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
genomic: GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAGgtgctttctt ... ttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
EST: gi|254332340|gb|GR846385.1|GR846385
EST:     GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAG                         ATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
genomic: GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAGgtgctttctt ... ttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
                     tgttaac  putative branch site (score: 2)
                                       ccttattt  putative PPT
                    atgttaacttattt  TA-rich tract