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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaatggctaagatgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC

Basic information

species Glycine max
transcript GLYMA19G45140.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 3'ss of exon 7
--------------gtgagaa-tggctaagatgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
              |||| || |  | |  |   |    |||| |  | ||    | |   | |||      |||| ||      ||  |||  || |  |  | ||||||||||| || ||||| ||||||||||| || || ||||| |||||||| ||||| ||||| || || |||||||| ||||| ||||||||||||||||
gtatgtgcaacattgtgaaaactcacaagaacttatcaattttctgcacttaaagtgcttctgtttgacaagcatgtttctgaaaaaaaaaatgttgacttggtttagATGGCCCGCTCGAAGAAAGCATGCATTGTCTTCTTTGATGAGGTTGATGCTATTGGAGGTGCTCGCTTCGATGATGGGGTTGGGGGTGATAATGAGGTTC

upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
gtgagaatggctaagatgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
         |  ||   | |     ||  |  | ||||||||| |       ||||  |  |||||   |||  ||||| || | |  | ||||||||||| |||||||||||||||||||| || || |||||||||||||||||||| ||||| || ||||||||||| ||||| ||||| |||||||| |
-----ggctgtgaatccgtaaaaggttcatccagtttttttcctgca---cacatgttaatatttc--tgaaacaaaatattctat--tgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
gtgagaatggctaagatgcactttttttttaaattttttttcccgttatttccatg---acatg---atttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
    | ||  ||| |  ||  |   |   ||||   ||  ||| ||| ||| | ||   |||||   || |    |||  ||||| || | |  | ||||||||||| |||||||||||||||||||| || || |||||||||||||||||||| ||||| || ||||||||||| ||||| ||||| |||||||| |
----gtatatctagg--gctgtgaatccgtaaaaggttcatccagtttttttcctgcacacatgttaatatttctgaaacaaaatattctat--tgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
--gtgagaatggctaaga---tgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
   |    ||||||  ||   || |  | || |   | | ||||         | |     |||| |||||   ||| | || | || | |  |  |||||||||| |||||||| || |||||||| || ||||||||||||||||| ||||| ||||| || ||||||||||| || || || || |||||||| |
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtac-gtgtgttcaacat-atttc--tgaaatgaattcttctatggt--agATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
gtgagaa--tggctaagatgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtc-ctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
|| | ||  || |  |  |  ||  ||| | |  |||| ||||   |||  ||          || |  ||  |||   |  || | |  ||  ||||||| || || || || || || ||||||||||| |||||||| ||||| || |||||||| || ||||||||||||||||| || || |||||||| |
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgtt-cttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC

upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 7
gtgagaatggctaagatgcactttttt---tttaaattttttttcccgttatttccatgacatgatt-tcatcgaactaaaattttatgtcctct------agATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
|||  |||   ||   |  | || |||   |  | |||  |||||  || |  |   |   |||||| |||| |  | |    |  ||||    |      ||||||| |||||||||||||| |||||||| ||||| ||||| || ||||| ||||| ||||| |||||||| |||||  | || ||||||||||||||||
gtgctaat--ttattgtttatttgtttagatgaacattagttttcatgtgacgtattttg-atgattctcatggtgcaacctgtccatgttacttgtgagcagATGGCTCGTTCAAAGAAGGCCTGCATTGTATTTTTTGATGAGGTAGATGCTATTGGAGGTGCTCGGTTTGACGATGGATTGGGGGGTGATAATGAGGTTC

upper sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
--------gtgagaatggctaagatgc-----actttttttttaaattttttttcccgttattt-ccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
        ||     |  || | | ||     ||| | | || |  |    |    || |  ||  | ||    |||||  |   |   || || |  |      ||||||||||||||||||| || |||||||||||||| ||||| || ||||| ||||| ||||| || || || |||||  | || |||||||| |||||||
ccgccagtgtattgtttactcaaacgctaagtactgtgtattcacgtggcctacttcgatgcttatcgtggtgcgatttgttt--atggaacttgtgag-----cagATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC

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|208281430|gb|GE078506.1|GE078506
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgagaatgg ... tgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
EST: gi|18040702|gb|BM308996.1|BM308996
EST:     TTCAGAAATATGTTGGTGAAGGTGCTCGAATGGTTCGTGAAATATTTCAG                         AAGGGCCCGTTCAAA-AAGGCATGCATTGTGTTTTTCAAAGAAAGT-GATG
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgagaatgg ... tgtcctctagATGG-CCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAA-GTTGATG
EST: gi|192295887|gb|FG992653.1|FG992653
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgagaatgg ... tgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
EST: gi|254320309|gb|GR831117.1|GR831117
EST:     TGAACTATTTCAG                         AT-GCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TGAACTATTTCAGgtgagaatgg ... tgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
EST: gi|254337400|gb|GR849353.1|GR849353
EST:     TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TTCAGAAATATGTTGGTGAGGGTGCTCGAATGGTTCGTGAACTATTTCAGgtgagaatgg ... tgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
EST: gi|254337401|gb|GR849354.1|GR849354
EST:     TCGAATGGTTCGTGAACTATTTCAG                         ATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA
genomic: TCGAATGGTTCGTGAACTATTTCAGgtgagaatgg ... tgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcccgttatttccatgacatgatttcatcgaactaaaattttatgtcctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC
                                aactaaa  putative branch site (score: 2)
                                             tgtcctct  putative PPT
                                aactaaaattttatgt  TA-rich tract