Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA

Basic information

species Glycine max
transcript GLYMA04G42800.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.1 (Oryza sativa), 3'ss of exon 1
----gtaacatt-atcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
    ||  | |  |||| |  | ||  ||  || |  | |  ||  |  |  |||||  ||  |      ||      | ||||| ||||    ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| ||  |||||||||| || || ||  |||| ||
gtacgtctcttccatctccctcctcc-atccatgcaaacttatagctactg-ttcatcgatcgtcca---tgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g66120.1 (Oryza sativa), 3'ss of exon 1
-----gtaa--cattatcttcaacttctgatatattcttattcttaattc---------ttaattcattcattt--tttgaattgt---tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
      |||  |     || || | ||  |   ||    |   | ||  |         || ||| ||| ||||  ||||| ||||   | ||||  |||  ||||    ||||||||||| |||||||||||||| || || || ||||| || ||||||||||| ||  |||||||||| || || ||  | || ||
gtacgataatcctcctcctccatcctcccaatcatcaccaccatcaacgccgtcgtgaattgattgattgatttggtttgatttgttggtgttgtgtagGGATGGCGCTGTACGGAGAGAAGGAGTGGTACTTCTTCTCCCCGCGAGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCGGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os05g34830.2 (Oryza sativa), 3'ss of exon 1
---------gtaacattatcttca-acttctgatatattcttattcttaattctt---aattcat--tcattttt--tgaattgttattg------tacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
          |  |||   |     || |||  |  ||     | ||  || | |   || | ||    | | ||  |  || ||   ||      | ||||| ||||    ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| ||  |||||||||| || || ||  |||| ||
gttcgatccatggcatctcccaagtacgtctcttccatctccctcctccatccatgcaaacttatagctactgttcatcgatcgtccatgactccatgcagGAATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCTCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGGTCCGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
----------gtaacattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttattgt-acagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
          | || |  |  |  ||        |     ||    |  | |   |||||| | | ||   || |||  |||||  |||    |||       || ||||| |||||||||||||| || || ||||||||||| |||||||||||     |||||||| |||||||||| || || ||
gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G014653_T03 (Zea mays), 3'ss of exon 1
------------------------------------gtaacattatc--ttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
                                    ||| ||         ||| |||   |     | |     |        | ||  ||  ||  | | |   | | || ||||  ||||    ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| |||||||| ||||| || || ||  | || ||
gtacgtcccgtcgtcctcggtcttcttgcagcagcagtagcagccgtgaaccaatttcctgtgcggccgtgacgatggcgagctaatcgatcgattgctaactctctgt-gtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCCAGGCCCAACCGCGCCGCCGGGGCTGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 1
--------------------------gtaa-cattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttat-tgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
                          | |  | || |       |||| |  |   | | | | |  | || | | |     |   |   | || | | ||| ||||  ||||    ||||| ||||| |||||||||||||| || || |||||||| || ||||||||||| ||  |||||||||| || || ||  |||| ||
gtacgtgtcgtccgccgccgctccacgcagtcgttgttccaggtttcttagctcgccctgtacctgctgctgactcctgatctcggtactactgctgtctgtgcagGGATGGCGCTGTACGGCGAGAAGGAGTGGTACTTCTTCTCCCCGCGGGACCGCAAGTACCCGAACGGGTCGCGGCCGAACCGCGCCGCCGGCGCCGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G123667_T05 (Zea mays), 3'ss of exon 1
-----------------------gtaacattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttga-attgttattg-----tacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
                       || |     | ||     || ||  ||      |    |   |    |    ||||    ||  || || || |     | |||    ||| | |   || ||||| |||||||||||||| || || || ||||| || |||||||| || |||||||| ||||||||||| || || || ||
gtacgtcgaacaatcggatcatcgtcagcgagtgttagttatccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA

upper sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g02300.t01 (Vitis vinifera), 3'ss of exon 1
----gtaacattatcttcaacttctgatatattcttattcttaattcttaattcattcatttttt---------gaattgtta--ttgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
     ||  ||||| ||||  || |  | |||| || |||| || ||  ||    |  ||||||          || ||| |   ||| ||||   |||| |  ||||||||||||||||||||||||||||| ||  | || |||||||| ||||||||||| |||||||||||||| |||||||| || ||
gtaattattattattttcatttttttgt-tattttt-ttctgaactcccaaaatttggatttttatttaagggggatttggtgatttgaacagAGATGGCCTTGTACGGAGAGAAAGAGTGGTACTTCTTTTCGCCGAGAGATCGGAAATATCCGAACGGTTCAAGGCCGAACCGGGCAGCGGGAACAGGGTA

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|17401487|gb|BM178269.1|BM178269
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|254345506|gb|GR851668.1|GR851668
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|19453464|gb|BM954874.1|BM954874
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|15812832|gb|BI785107.1|BI785107
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|209708546|gb|BW668157.1|BW668157
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|20811624|gb|BQ296102.1|BQ296102
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|254338578|gb|GR845721.1|GR845721
EST:     CGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|298172091|gb|HO021683.1|HO021683
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|19453545|gb|BM954955.1|BM954955
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|20811728|gb|BQ296206.1|BQ296206
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|298181418|gb|HO022857.1|HO022857
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|261497080|gb|GT185255.1|GT185255
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|298171680|gb|HO021272.1|HO021272
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|298179565|gb|HO028036.1|HO028036
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|298184586|gb|HO029799.1|HO029799
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
EST: gi|254319224|gb|GR830572.1|GR830572
EST:     CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCG                         GATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC
genomic: CATCATCGCCGAAATCGACCTCTACAAATACGACCCCTGGGACCTACCCGgtaacattat ... tattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatattcttattcttaattcttaattcattcattttttgaattgttattgtacagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA
                  tcttaat  putative branch site (score: 3)
       ttattcttaattctta  TA-rich tract