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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

Basic information

species Glycine max
transcript GLYMA04G38560.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagtt-caattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
                 |  || || ||   | |    ||     | ||   | | | ||| | |  || || |||  |   |   || |||||| ||| |   | ||||||||||| || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||||||||||||||   ||| ||
----------------gtacgtctc-ttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
gttcgtt---tagtttcttatgggt---ttcgttttgtgtgaaaccaattccaattgtatcgtttagtt-caattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
||||| |   | |  |||     ||   |   ||   | |    ||     | ||   | | | ||| | |  || || |||  |   |   || |||||| ||| |   | ||||||||||| || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||||||||||||||   ||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagt--tcaattgattgattatga---gttggt-caatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
|| || | |   || |      | |      |     ||||    |||     ||||  | |  |  |||||||   | |||   ||||||    || ||  || |   | ||||| ||||| || ||||||||||| || || || ||||| || ||||||||||| || ||||||||||||||||||||    || ||
gtacgataatcctcctcctccatcctcccaat-catcaccaccatcaacgccgtcgtgaattgattgattgatttggtttgatttgttggtgttgtgtagGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
        |    |  | |    |||  | |  |  |   ||||  | | | ||  |  | ||||||| ||||   ||  |    |   |||||| |  |   |    || ||||| || ||||||||||| || || ||||||||||| |||||||||||    ||||||||| | || || || |  || ||
--gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaat--tcaaattcaattaattggggatttgg-aattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
---------gttcgtt-tagtttcttatgggtttcgttttgtgt---gaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
         || ||     | | |     |   | |||    ||     | |     |      |   | | | | |   |  | | |  |      |||  |||||  || |   | ||||||||||| || ||||||||||| || || |||||||| || ||||||||||| || ||||||||||||||||||||   ||| ||
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatc-tcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G014653_T03 (Zea mays), 3'ss of exon 1
-----------gttcgtttagtttcttatgggtttcgttttg--tgtgaaaccaattcc-----aattgtatcgtt--tagttcaattgattgatta-tgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
             || |     |||||   |     ||       ||||| | | ||||         ||  || |        ||| ||| ||||  | | |   |   |||||  || |   | ||||||||||| || ||||||||||| || || |||||||| || ||||||||||| ||  |||| ||||||||||||||    || ||
gtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgtgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCCAGGCCCAACCGCGCCGCCGGGGCTGGGTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 1
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
|| |   ||    ||| |     |  ||||  | |||| ||  |    | |       | ||| | |    || ||    |||  ||  | |||| ||   | | ||||| |||||||| ||||||||||| || ||| | || ||||||||||| |||||||| || || ||||| || || |||| ||| ||
gtacacctatgggcttcttctaattatttttcgcgaaatcatgtgtcttcgagaatcgttgtttattgagatgttt----gttcttcttt-cagAGATGTCTCTGTACGGAGAGAAAGAGTGGTACTTCTTCTCACCTAGAGATCGGAAATACCCAAACGGTTCGCGTCCTAACCGGGCAGCAGGAACCGGTTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 1
--gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
       || |||     |   | ||    |   ||      ||||   | | |    ||| |        |  || |  || ||  |   | ||||||| |  || ||||| |||||||||||||||||||| || | | | |||||||||||||| ||||| ||  | || ||||| || || |||| ||| ||
gtaaaacttcagtccacgacaagattgacatatggttttgtgaatt--gactttgagattttg-------aagagaattcgaatttttgtttccagAAATGGCGTTGTACGGTGAGAAAGAATGGTACTTCTTCTCGCATAGAGACCGGAAATACCCAAACGGGTCGAGACCAAACCGGGCAGCTGGAACCGGTTA

upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 1
---gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaatt--gattgattatgagttgg-tcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
    || |   | | |  |      |  ||     ||    | | |||      | |     |  | ||||  |||   ||  || |||| |   ||||| ||| | | | ||||| || || || ||||||||||| |||||  ||||||| ||||| || ||||||||| |||| ||||| || ||||||  ||||||
aatttttgacaaatatgatcgaaactctgtaaatcgtctctctagttcagcaaattttcagaaactgaatttggatatttttggaattgggtttctgcagGAATGGCTCTGTACGGTGAAAAGGAGTGGTACTTCTTCTCTCCAAGGGACCGCAAATATCCCAACGGTTCAAGGCCTAACCGGGCGGCCGGATCCGGCTA

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|120533637|gb|EH261770.1|EH261770
EST:     CGTCATCAAAGAGGTCGATTTGTACAAGTTTGATCCATGGCAGCTTCCAG                         AAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACC
genomic: CGTCATCAAAGAGGTCGATTTGTACAAGTTTGATCCATGGCAGCTTCCAGgttcgtttag ... gtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA
                             gattgat  putative branch site (score: 4)
                         aattgattgattat  TA-rich tract