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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacataatcattcattcattcattcattcttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA

Basic information

species Glycine max
transcript GLYMA06G11970.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
gtaacataatcattcattcattcattcattcttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
     |      |||  ||  ||  || | | || ||  |  | |  ||  |  | || ||  || ||  |  ||   |  | ||||| ||||    || || ||||| |||||||||||||| || || |||||||| || ||||| ||||| ||| |||||||||| || || ||  |||| ||
---gtacgtctcttccatc--tccctcctccatccatg-caaacttatagctactgttcatcgatcgt--ccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
---------gtaacataatc---attcat-tcattcat-tcattcttcgatttctg---attcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
          |  |||   |    | | | || | ||| ||  || || ||   ||   | |  ||  |  | || ||  || ||  |  ||   |  | ||||| ||||    || || ||||| |||||||||||||| || || |||||||| || ||||| ||||| ||| |||||||||| || || ||  |||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgt--ccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
gtaacataatcat--tcattcattcattcattcttcgatttc-tgattcttaatttttatttattaattgttactgtgttactt----------tacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
|||  |||||| |  || | ||| |   || || ||     | | |         |  ||| ||| |||| |   || | | ||          |  |||  ||||    || |||||||| |||||||||||||| || || || ||||| || ||||| ||||| ||| |||||||||| || || ||  | || ||
gtacgataatcctcctcctccatcctcccaatcatcaccaccatcaacgccgtcgtgaattgattgattgatttggtttgatttgttggtgttgtgtagGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
gtaa-cataatcattcattcattcattcattcttcgatttctgattcttaatttttattta-ttaattgttactgtgttact-ttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
|||| ||  | ||       ||  | ||       |     |||     ||||   ||| | |||||||    | ||  | | || |||    ||| |     || ||||| |||||||||||||| || || ||||||||||| ||||| |||||   | |||||||| ||||||| || || || ||
gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA

upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
---------------------gtaacataatcattcattca--ttcattcattc-ttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
                        ||  | || ||  | ||  ||  ||   ||   |  |  ||| | || | |  | || |    | |  | ||||    || | ||||  ||||    || || ||||| |||||||||||||| || || |||||||| || ||||| ||||| ||| |||||||||| || || ||| |||| ||
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgt----ctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA

upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G014653_T03 (Zea mays), 3'ss of exon 1
------------------------------gtaacataatcattcattcattcattcattcttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
                              | | ||  | ||  | |  |   |||   | | ||                  | ||  ||  |||| ||      |  | | ||||  ||||    || || ||||| |||||||||||||| || || |||||||| || ||||| ||||| || ||||| ||||| || || ||  | || ||
gtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctg-tgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCCAGGCCCAACCGCGCCGCCGGGGCTGGGTA

upper sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g02300.t01 (Vitis vinifera), 3'ss of exon 1
-------gtaacataatcattcattcattcattcattcttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
        ||  ||  |||||  ||  ||  ||  ||||    |  |  | | |  |||||||||||       ||   ||| |  |  ||||   ||||    || |||||||||||||||||||||||||| ||  | || |||||||| || |||||||| |||||||||||||| || || || || ||
gtaattattattattttcatttttttgttatttttttctgaactcccaaaatttggatttttatttaagggggatt-tggtgat-ttgaacagAGATGGCCTTGTACGGAGAGAAAGAGTGGTACTTCTTTTCGCCGAGAGATCGGAAATATCCGAACGGTTCAAGGCCGAACCGGGCAGCGGGAACAGGGTA

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|58024693|gb|CX711434.1|CX711434
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGTCCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|298168446|gb|HO009376.1|HO009376
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|213605648|gb|DB972296.1|DB972296
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|58021107|gb|CX707849.1|CX707849
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGTCCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|21678264|gb|BQ630615.1|BQ630615
EST:     CATCATCGCCGAAATCGACCTCTACAAATATGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGCACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|18734175|gb|BM528031.1|BM528031
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|209709358|gb|BW668328.1|BW668328
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|254344238|gb|GR851041.1|GR851041
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|213592475|gb|DB971631.1|DB971631
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|213595443|gb|DB966539.1|DB966539
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|209713052|gb|BW653759.1|BW653759
EST:     CATCATCGCCGAAATCAACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|213592504|gb|DB971646.1|DB971646
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|209713140|gb|BW653849.1|BW653849
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|209727657|gb|BW663797.1|BW663797
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|209727697|gb|BW658434.1|BW658434
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|11274975|gb|BF325299.1|BF325299
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|11273926|gb|BF324315.1|BF324315
EST:     CCCCTGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|23064618|gb|BU579391.1|BU579391
EST:     CATCATCGCCGAAATCGACCTCTACAAATACTACCTCNGGGACTTACCCG                         GATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACTTACCCGgtaacataat ... tactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgatttctgattcttaatttttatttattaattgttactgtgttactttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA
                           tattaat  putative branch site (score: 2)
                                            ttacttt  putative PPT
               ttaatttttatttatt  TA-rich tract