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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG

Basic information

species Glycine max
transcript GLYMA15G18170.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g13690.1 (Oryza sativa), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                                     | | | |  ||  |   |       | ||||||||| |    ||    |  ||    | |      | ||     | || ||||||||||||||| | ||||| || ||||||||  ||||||||||||| ||||| |||
------------------------------------gtgagaaactataccgctacggcttaaaattgtctttgtttgcataa--gcattgacagttcgctatgcttt----atgt-agTATCAATGCCATGCACCCCAAGACCAGGAAGATCTTGCAGCTTCTGCGGTTGAGGCAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G868433_T02 (Zea mays), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                               |  |   ||    | ||| ||  ||  |         | | | || ||||  ||||||||      |||  ||||   | |||  |||||||||||||||| |||| || || ||||||||  ||||||||||||||||||| |||
-----------------------------gtgagtcgcaagtgcttatgccagtattatgtagaggaatttgtatgattatgcttgttttt------aattccgtt---gaaactacagTATCAATGCCATGCATCCTAAGACCAGGAAGATATTGCAGCTTCTGCGTTTGAGGCAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G13580.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                  || || | || || ||||   || |  || |  || |   |  | | ||   | | |   | || |   |  | || |||      | | | || | |||||||||||||||| || || || |||| ||||||| |||| ||| ||||||| ||||||
-----------------gtaata-tgatctactattactatctcccaag-tataaggatgatgtgttacttctataactgttttc--tcatttttctatctatttgtttctatcatcagTATCAATGCCATTGACCCAAAGACAAAGAAGATTTTGCAACTTTTGCGTTTAAGACAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G01250.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                ||| |||      || | || |  | | || |   | ||| |    |    || | | ||    |||||||| || |  ||  ||   ||| |   |   ||||||||||||||| || || || || | ||||||||| |||||  ||||||||||||||
---------------gtatgtta------tactgttgttgtttgtcttataagcatttctaaagccagtgtctatg----ttgttgttcttat--ctgttgttctttttaatattgcagTATCAATGCCATTGACCCTAAGACTAAGAAGATTCTCCAGCTCTTGCGTTTGAGACAG

upper sequence: GLYMA15G18170.2 (Glycine max), 3'ss of exon 3
lower sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                     ||  |   || |||||   | |  ||| |  |  |     || ||| | |||||  ||   ||  || ||        || | |||         ||||||||||||||| || || ||||| | ||||||||||||||| |||||||||||||||
--------------------gtatgtgcctattatttgtgtgttacataagttgttgcatatagattctgttttttatttacgtgattgtt--------tgtcatttg--------cagTATCAATGCCATTGACCCAAAAACCAAGAAGATTCTGCAGCTCCTGCGTTTGAGACAG

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|8282865|gb|BE020426.1|BE020426
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|209702466|gb|BW667098.1|BW667098
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|17023603|gb|BM094637.1|BM094637
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
EST: gi|298195246|gb|HO043774.1|HO043774
EST:     TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGG                         TATCAATGCCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT
genomic: TTTTATGTTGAACCCGAAGCTAAGCTCTTGTTCATCATCAGGATCCGTGGgtaattaatc ... gtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG
                                        tttctgt  CT-rich tract
             ttattgttgttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaatcaataaatatattaattatttagtattttaatatatcatgacatcatattagtatattgtctttttggttattgttgtttttcttgctaatggcgtttctgtaacgtcagTATCAATGCCATGGATCCCAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT