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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattacatgatttttttgcatgctcttgttaaagtatatagtacatatgagcacatttcaccatacatattcaagatttatttgttgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA

Basic information

species Glycine max
transcript GLYMA16G01660.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
--------gtaattacatgattt--ttttgcatgctcttgtta-aagtatatagtacatatgagcacatttcaccatacatattcaagatttatttg---ttgatatg------cagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA
        |   |   ||| |||  | |  ||| |  || |   ||  | |    |  | |   |  | || | |||  | ||  |||||  |  |    |||| ||       |||||||||||||| || ||||| ||||| ||||| || ||||| ||||||||||||||||| |||| ||  |||||||| |||||| |||| || 
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattga-atgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG

upper sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G12370.1 (Arabidopsis thaliana), 3'ss of exon 17
gtaattacatgatttttttgcatgctcttgttaaagtatatagtacatatgagcacatttcaccatacatattcaagatttatttgttgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA
|||||| | |   |||| |   |     | ||  |    ||  ||    |  |   | || |  |||         | ||  ||  ||| |   |||||||| || || || ||||||||||||||||| || | ||| |||||| |||||||||||||||  || |||||||| |||||  |||| || 
gtaattccttctcttttctatttctcactatttgaa---atgctattgttatgtggagttaattata---------gtttctttgattgtttctcagGCAGAAGCTGCTGCTGCTGCTGGTGAAAGTAGCTTTAAATCCTTCATGGTTGCTGTGCAACGTTGCGGTAGCAGTGTTGCTATAGTTCAGCAG

upper sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 16
-------------------------------------------------gtaattacatgatttttttgcatgctcttgttaaagtatatagtacatatgagc-acatttcaccatacatattcaagatttatttgttgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA
                                                  ||  ||| | | ||   || ||   ||| ||| |   ||| | | |  | | | | |  | | |   ||||    ||| ||  ||  |||| || ||||||| || || || |||||||||||||| |||||||||||||||||| | ||||| || |||| ||  |||||||| |||||| |||| |||
gtaattacttgatcacatggccattttctgcattttaaaatttactctactacatacctcaattcaatgtatatgcttcttagaaagtattgaataatttatctagaaattatcgggcataa--gagaatttgttactgatgtgtagGCAGAAGCTGCTGCTGCTGCTGGTGAAAGCAGTTTCAGATCTTTCATGGTGGCTGTACAGCGTTGTGCTAGCAGTGTGGCTATTGTTCAGCAA

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|193680324|gb|FK624832.1|FK624832
EST:     TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCT                         GCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
genomic: TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCTgtaattacat ... tgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
EST: gi|192329176|gb|FK019763.1|FK019763
EST:     TGCTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCT                         GCAGAGGCGGCAGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTTATGATT
genomic: TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCTgtaattacat ... tgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
EST: gi|15287423|gb|BI471314.1|BI471314
EST:     TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCT                         GCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
genomic: TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCTgtaattacat ... tgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
EST: gi|208340156|gb|GE133198.1|GE133198
EST:     TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCT                         GCAGAGGCGGCGGCAGCTGCTGGTGAAAGT-GTTTCAGATCTTTCATGATT
genomic: TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCTgtaattacat ... tgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
EST: gi|208165639|gb|GD964117.1|GD964117
EST:     TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCT                         GCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT
genomic: TGTTGGGTACAAGTGTTACCCGTAGAGTGGCTGCTGCAGCTGCATCTGCTgtaattacat ... tgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacatatgagcacatttcaccatacatattcaagatttatttgttgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA
                                          tgttgat  putative branch site (score: 4)
                      atacatattcaagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattacatgatttttttgcatgctcttgttaaagtatatagtacatatgagcacatttcaccatacatattcaagatttatttgttgatatgcagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG