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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgccaattgtgaattgcttattgaattgagtattgaacattatgtgtgaattttacaaatgccttgttttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT

Basic information

species Glycine max
transcript GLYMA0048S00290.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g49690.1 (Oryza sativa), 3'ss of exon 7
--------------------------------gtaatgccaattgtgaat-tgcttattgaattgagtattgaacattatgtgtgaattttacaaatgccttgttttca-----tgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT
                                 |  | |  |  |||  |    | | |  |||  | ||     ||||  |||     ||  |||||  ||   |  |     ||||||||||  | || |||||||| ||||| ||||| || || ||||| || ||||| |||||  | ||||| ||||| ||||| |||||||||||||||
gtatgtacagtcatttgatgatttcttactctatttttcagagagtgtgtacagtcactacattctggatcatctattaattgttt-ccttgtaaatgtttttcatctaccttttgcagTTCAACCATATTAACAATCTCGATCTAGTTTGCCGAGCTCACCAGCTGGTTCAGGAAGGCTTAAAGTACATGTTTCAGGACAAAGGCCTTGTAACT

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 7
lower sequence: AT1G50370.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatgccaattgt-----gaattgcttattgaattgagtattgaacattatgtgtgaatttta-----caaat-----gccttgttt-tcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT
||| |   | || |     |  |||    ||||||   || |  ||    ||   || |||| |     |  ||     |  ||| || |  ||||||| ||  | || |||||||||||||| || ||||| || ||||| || || ||||||||||| ||||| |||||||| |||||||| |||||||||
gtatttatatttttttctggggttgaaatttgaataaggtgtgaaaagaaataaatgtatttcagttccctgatctgtggttttgcttcttgtgcagTTTAACCATATTAACAATCTTGATCTAGTATGTCGCGCTCACCAGCTTGTACAAGAAGGTCTCAAGTACATGTTCCAAGATAAAGGTCTTGTAACT

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 7
lower sequence: AT3G19980.1 (Arabidopsis thaliana), 3'ss of exon 7
----------gtaatgccaattgtgaattgcttattgaattgagtattgaacattatgtgtgaattttacaaatgccttgttttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT
           |  |   ||   ||||||| |  |  || | || | | ||  | |  | |    | |     | |    || |  ||||||| ||  | || ||||| || ||||| || || || || |||||||| || ||||||||||||||||| |||||||| ||||||||||||||||||
gtatgtttactttctcaaaagcttgaattgatactgtaactaagaaattaatttcacatctctgatctttgg-ttctggcttcttgtgcagTTTAACCATATCAACAAGCTGGATCTAGTATGCCGCGCGCACCAACTTGTACAAGAAGGTCTTAAGTACATGTTCCAAGATAAAGGCCTTGTAACT

upper sequence: GLYMA0048S00290.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv10s0071g00950.t01 (Vitis vinifera), 3'ss of exon 7
gtaatgccaattgtgaattgcttattgaattgagtattgaacattatgtgtgaattttacaaatgccttgttttcat-gcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT
         |  ||||     |    |  | |  | ||  | | |   |||    |    || |   ||  |||| |  ||||||||  |||||||||||||||||||||||||||| || ||||| || || ||||||||||| ||||| ||||| ||||||||||| || ||||| 
-------gtagagtgatacaatctcggcttcgtcttttccagacttcatgtttgctgaggaattttttttctttctttacagTTCAACCACATAAACAATCTTGATCTGGTTTGTCGAGCCCACCAGCTTGTACAAGAAGGTCTAAAGTACATGTTTCAGGATAAAGGACTCGTAACC

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|151410851|gb|EV280666.1|EV280666
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|192323250|gb|FK018961.1|FK018961
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCG
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCG
EST: gi|254337376|gb|GR849329.1|GR849329
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|16345163|gb|BI970758.1|BI970758
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|192296025|gb|FG989419.1|FG989419
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|254340657|gb|GR854385.1|GR854385
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|209728248|gb|BW651683.1|BW651683
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|213611336|gb|DB983956.1|DB983956
EST:     CTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: CTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|213593175|gb|DB975366.1|DB975366
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|193307325|gb|FK271109.1|FK271109
EST:     CAGTCCTCGTGGAGCTGGTTGGTCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: CAGTCCTCGTGGAGCTGGTTGG-CTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|5753202|gb|AI960489.1|AI960489
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
EST: gi|31473271|gb|CD415284.1|CD415284
EST:     CAGTCCTCGTGGAGCTTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACTATCTTGATCTGGTTTGTCNGGGCACACCAACTCGT
genomic: CAGTCCTCGTGGAGC-TGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTC-GGGCACACCAACTCGT
EST: gi|254340656|gb|GR854384.1|GR854384
EST:     TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAG                         TTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT
genomic: TCAGTCCTCGTGGAGCTGGTTGGCTTTTTGGATCCCGGGTCACTTCTGAGgtaatgccaa ... tttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgagtattgaacattatgtgtgaattttacaaatgccttgttttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT
                                       ccttgttttc  CT-rich tract
                        tgaattttacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgccaattgtgaattgcttattgaattgagtattgaacattatgtgtgaattttacaaatgccttgttttcatgcagTTCAATAACATAAACAATCTTGATCTGGTTTGTCGGGCACACCAACTCGTTCAAGAAGGTCTTAAGTATATGTTCCAGGATAAAGGCCTTGTAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG