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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG

Basic information

species Glycine max
transcript GLYMA09G24530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G163683_T01 (Zea mays), 3'ss of exon 2
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG----------------------------
           | |       |  ||   |   ||  ||  | |  || |  ||||   |||   |               | |||  | || ||    | |    ||||   ||| |   | ||||| || |||||||| |||||  | ||||| ||| |||| |||||||| || ||||||||||||||||| |||                            
----------gtacgcggcggtccttggcagctcagctctatctccaactttttttcctttcctgac--------------gcgaaactgggctg----acttccctgggcgcgtccg---tgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT

upper sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G163683_T02 (Zea mays), 3'ss of exon 2
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG----------------------------
                                 ||  ||  | |  || |  ||||   |||   |               | |||  | || ||    | |    ||||   ||| |   | ||||| || |||||||| |||||  | ||||| ||| |||| |||||||| || ||||||||||||||||| |||                            
------------------------------gctcagctctatctccaactttttttcctttcctgac--------------gcgaaactgggctg----acttccctgggcgcgtccg---tgcagGTCGGGATGGAGTTCTGGGCGCGGTGGGCGCACCGGGCGCTATGGCACGCCTCCCTGTGGCACATGCACGAGTCGCACCACCGGTCGTGCGAGGGCCCAT

upper sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25700.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtga-gttctttgtgaattttgggtggtaga-ttcaattgggtatgtctgatt-ttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG
                                                      |    |||| || |   |     | ||| ||| |  |       | | ||    || |  | |  |||| ||||||| |||||||| || ||||| ||||||||||| || ||||| ||||| ||||| || ||| | |||||||||
-----------------------------------------------------gtaagtttcaaaacttcatcccaatttttctgattcataaacaaaaaagtttggctgagatttttggattattcagGTTGGTATGGAATTCTGGGCAAGATGGGCTCATAGAGCTCTGTGGCACGCTTCTCTATGGAATATGCATGAG

upper sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 2
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG
                          |  |    | |||| |    |    |   ||||  |  ||   |   |  ||  ||   |||  |  |  |  ||  | ||  |||| | ||| ||| |||| || |||||||||||||| ||||||||||| || ||||| ||||||| |||  | ||| |||||||||||
-----------------------gaaaaaaacgaagttcaataaccaga-acaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttat--attttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG

upper sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01090.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG
    ||||    | ||||   |     | |||    ||| ||||  | ||       || |||   ||| |  || |   | |||       | | |  ||  || | ||||| | | ||| |||||| || |||||||| ||||| |||||||||||||  ||||| ||||| || ||| | ||||||||||| |||
----gtaagtgcctttttccct-----tcattttccttcggtttctagtt-----ccaaatcatgtttgcg-aagctgggtttgaggcgattgcgttgaatcgaaataggtattttttattctcagGTAGGCATGGAGTTCTGGGCGAGATGGGCTCACAAAGCTCTCTGGCACGCCTCCTTATGGCACATGCACGAG

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|192299479|gb|FG988763.1|FG988763
EST:     TGCCTTTGTCTGAAATTTTTGGCACATTTGCTCTATCAGTGGGAGCTGCT                         GTGGGTATGGGAGTTTTGGGCTAGATGGGGCTCACAGGGCTCTATGGCATG
genomic: TGCCTTTGTCTGAAATTTTTGGCACATTTGCTCTATCAGTGGGAGCTGCTgtgagtaatc ... tgattttcagGTGGGTATGG-AGTTTTGGGCTAGATGGG-CTCACAGGGCTCTATGGCATG
EST: gi|17022679|gb|BM093713.1|BM093713
EST:     TGCCTTTGTCTGAAATTTTTGGCACATTTGCTCTATCAGTGGGAGCTGCT                         GTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCT
genomic: TGCCTTTGTCTGAAATTTTTGGCACATTTGCTCTATCAGTGGGAGCTGCTgtgagtaatc ... tgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCT
EST: gi|14992046|gb|BI317719.1|BI317719
EST:     GTGGGAGCTGCT                         GTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCT
genomic: GTGGGAGCTGCTgtgagtaatc ... tgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCT
EST: gi|27446214|gb|CA953337.1|CA953337
EST:     TGCCTTTGTCTGAAATTTTTGGCACATTTGCTCTATCAGTGGGAGCTGCT                         GTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCT
genomic: TGCCTTTGTCTGAAATTTTTGGCACATTTGCTCTATCAGTGGGAGCTGCTgtgagtaatc ... tgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAG
                                          gtctgat  putative branch site (score: 4)
                                                ttttc  CT-rich tract
           tgaatttt  TA-rich tract