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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcggtatactcttctagcattttaactgacacatatttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG

Basic information

species Glycine max
transcript GLYMA13G32940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g31190.1 (Oryza sativa), 3'ss of exon 3
gtgcggtatactcttctagcattttaactgacacatatttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
                ||   ||  ||   | | | | | ||| ||    || |    || |  |||  | ||  |||||  | |   | | | |     |||||||| || |||||||| || |||||||| || ||  | ||||| ||||| || || || |||   |||||||||||||||||||||||||| || || |
---------------gtacttttgcaatatataaacaatagtgcataccctttac---ttactttgtgatcactatgttaaccttgcttcaatgg---cctagTTGGACATCATGGACAGGGGCACTGATGCTCGTAACTTTTTACTGGGAAATGTGATCCCCCTCAAGCTTGGTTATGTAGGTGTTGTAAATCGTAGCCAAG

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 3
gtgcggtatactcttctagcattttaactgacacatatttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
||    | | |    |    ||||  | ||  |||| ||||   ||  | |    |   |||||     || || | || | |   |||| | |    |  ||||||||||||||||||| || ||||||||||||||  |  | || ||||| || || ||  |   |||||| ||||| |||||||| || ||||| ||| 
gtttttttttcctcgccttaatttcta-tgctacat-tttggccatcctatctctcctgtgccactcaatg-cagtctt-gtctgatgttgtgtttcttccagTTGGATATAATGGACAGGGGCACTGATGCCCGGAACTTTCTGCTGGGAAATGTGATCCCCTTAAAACTTGGCTATGTTGGTGTTGTTAACCGCAGCCAGC

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G129155_T02 (Zea mays), 3'ss of exon 3
gtgcggtatactcttctagcattttaactgacacata----tttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
||    | |    |||   ||  |||| |  ||  |     ||||   ||  | |    |   |||||     ||  ||   |    || |  | |||    |  ||||||| ||||||||||| || ||||||||||||||  |  | || ||||| || || ||  |    ||||| ||||| ||||| || || ||||| ||| 
gttttttctttctttccttcaccttaatttccaagttacattttggccatcctatctctcctgtgccactgattgcaatctattctgatgttctgtttct--tccagTTGGACATAATGGACAGGGGCACTGATGCCCGGAACTTTCTGCTGGGAAATGTGATCCCCTTAAAGCTTGGCTATGTTGGTGTCGTCAACCGCAGCCAGC

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G14120.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgcggtatactcttctagcattttaactgacacatatttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
||||  | |        |  | |||   | | |  ||  |||||    ||  || ||  | | || |      |||| |    ||||  | | ||  ||  |||||||||| |||||||||||||||||||| |||||||   | || ||||||   |||||||| |||||||| || || || ||||||||||| ||||| |
gtgctatttctctcctcataagtttgctttagatttagctgtga----tggcaaactact-ctatttctcacgattgct--ctattttctctctg--attcagTTGGATATTATGGACAGAGGTACTGATGCTCGGAATCACCTTCTGGGAAAAACAATTCCTCTTCGACTTGGATACGTGGGAGTTGTAAATCGTAGTCAAG

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgcggtatactcttctag-cattttaactgacacatatttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
||||    | |   || || |||||    |    |||     |     |   |    |     |||||  |    ||  ||    ||  ||||   |  |  |||||||||| ||||||| |||||||||||| || || ||  | || ||||| ||| ||||||| |||||||| || || || |||||||||||  | ||||
gtgcatattcccagtccagacatttgttttatttcatcaccataggcgtccctgtctt----tcatgtgat----ttactatatgtt-attatcatgttttcagTTGGATATTATGGACAAAGGTACTGATGCTCGAAAACTCCTTCTTGGAAATGTTGTTCCTCTTCGACTTGGATACGTGGGAGTTGTAAATCGTTGCCAGG

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 3
gtgcggtatactcttctagcattttaa-ctgacacatatttgtg-aattttgttaagctgttgccatgttctgacattgttaggcatttgtt--atttggaatgt-agTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
||||  ||||      |    ||||   || |   ||   |||| ||  ||   ||||| ||  ||| |||| |    ||| ||||  |     | ||| ||| | ||||||| || |||||||||||||| |||||||| ||| | || || |||||||| ||||| || |||||||||||  |||||||||| ||||| ||||| |
gtgctatatatcaacttgatttttttgtcttatgaatgcctgtgcaacatttgcaagcttttatcattttctaatgaggtttggcaaataccccacttgtaatttcagTTGGACATTATGGACAGAGGTACCGATGCCCGCAATTTATTGCTTGGAAAAGTGATTCCCCTTCGACTTGGTTACATAGGTGTTGTGAATCGTAGTCAAG

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S221_85V6.1 (Physcomitrella patens), 3'ss of exon 5
gtgcggtatactcttctagcattttaactgacacat-atttgtgaattttgttaagctgttgccatgt-tctgacattgttaggcatttgttatttggaatgt--agTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
       ||| | ||| | | | ||      |  ||      |  ||    | ||| | |||    |  | |   | ||||   |||| | ||  ||||||||  |||||||||||||||||||||| || || ||||||||| |  | || ||||| || || ||  | || ||||| ||| | || ||||| ||| | ||||| |
------catagttttcgaacgtattcgtcttcttattgagaatagatacattcaagttattgtagggcgtgtttaagtgtttt-cattgggtacctggaatgtgcagTTGGATATAATGGACAGAGGAACAGACGCCCGGAATTTCCTGCTCGGAAATGTCATACCATTACGTCTTGGCTATATTGGAGTTGTTAATAGGAGTCAAG

upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S101_111V6.1 (Physcomitrella patens), 3'ss of exon 4
-gtgcggtatactcttct---agcattttaactgacacatatttgtgaattttgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgt--agTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
 ||   |    |  || |   ||  ||||  ||   | ||    ||   |      ||| |  ||        ||| ||  ||   || | || |  | ||||||  |||||||||||||||||||||| || || ||||||||| |  | || ||||| ||| | ||  | || ||||| ||| | || || || ||  | ||||| |
cgtttagagggcctttttgggagtgttttttcttctaaatggaagtatttacatccaagttactgt-------tgaaatgatt--tcagtggtaaccttgaatgtgcagTTGGATATAATGGACAGAGGAACAGACGCCCGGAATTTCCTTCTTGGAAATGTTGTACCATTACGGCTTGGCTATATTGGAGTCGTTAACAGGAGTCAAG

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|7692076|gb|AW760191.1|AW760191
EST:     GTAATAGAACAATCGGTGTAATCACAAAG                         TTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAA
genomic: GTAATAGAACAATCGGTGTAATCACAAAGgtgcggtata ... tggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaagctgttgccatgttctgacattgttaggcatttgttatttggaatgtagTTGGATATAATGGACAGAGGTACTGATGCCCGGAATCTGTTACTAGGAAAAGTTATTCCTCTCCGACTTGGTTATGTAGGTGTTGTAAATCGCAGTCAGG
                  ttctgac  putative branch site (score: 2)
                                   atttgttattt  TA-rich tract