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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG

Basic information

species Glycine max
transcript GLYMA20G24790.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
----gttt-gtgctc-tccacttccttgctagtgt-gggtgcattt-tgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
    |||  ||| |  |  | ||  ||  || ||  |  || |    ||| |  |  |   |||   | |   | ||| |||||    |   | ||| |||||    |||||  | || || ||||| ||||||||||| ||||| ||||| || ||||| || || ||||| |||||||| ||||| ||||||
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgttt-ttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 9
---------------------------------------------gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgca---tattgcacatgactgtttttgttaacaaccttagtt---attgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                             || |      ||   |  |||       || |||||| ||||    || |   |||||   |  | |||   | | |  |||   | ||   |||  ||||   ||||||  | || || || |||||||||||||| |||||||| ||||| ||||| || |||||||| |||||||| ||||| ||||||
gtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtct-ttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 9
---------------------------------------------gtttgtgc-tctccacttccttgctagtgt----gggtgcattttgggaactgc-atattgcacatgactgtttttgttaac-aaccttagtt---attgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                               |   || |||   ||| |   || || |    | |||||| | ||  | ||  || |      | |  ||||   ||||| ||||  | ||   |||  ||||    |||||  | || || || || ||||||||||| |||||||| ||||| || || || |||||||| |||||||| ||||||||||||
gttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaaccaaaatttggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                                                        |  || |||       ||   ||   ||  | | |  | |   ||   || || | ||      |     || ||| | |  |   |  |||||   || ||  | || || | ||| || || || || ||  |  | || |||||||| ||||||||||| ||||| || ||||||||||||
gtgcataaataatttcaccaaccattattacacaagttccattaatgcagaaaccatgcatactatttctaatgatggtctttttagtctatataagttgaattcttgattgattctatgtaatgta-atagtgactcaaaataccaaacatt-tggcttcagGTTTTCTCGATCAGAGATGCTGGTGCCAATAATTTAAAGCGTTTGACAGAGGAATTTGGCCCTGAGTGGGCGATGCAACATATAATTCCTCAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatg-actgtttt---tgttaacaaccttagttattgt-agGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
      |  |  || |||  | |     | |   |||   |  || |  || |  |   |  |||| ||    | || | |   |||   ||||| ||||||| ||||| || ||||| ||||| |||||  |||| || ||||||||||| ||||| ||||| ||||| |||||||| ||| ||||||||
------gtccctca-ttctctaccttcattgaatcatccagataaataaatttgtcgtctctactgcttgaaattttgaaataattataaattgtcagGTTCACTCAATCCGTGAAGCTGCTGCAAACAATCTGAAGCGTCTTGCTGAAGAGTTTGGTCCTGAATGGGCAATGCAGCATATAGTTCCTCAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G25800.1 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                                  | |     | | |   | |||  |  |     |  |||||      |   | ||     |   | ||||| ||  |        | ||  |||||||| ||||| ||||| || |||||||||||  | || || |||||||| |||||||| ||||| ||||| ||||| || ||| ||||||||
gtatttctttctctctcttacttttactgggaatgatcagattataccgcttcttatttatagaaattgatttt-----tttttttttttttttttttttttttttttgcggatgctctcat--tagGTTCACTCAATCCGCGATGCTGCTGCTAACAATCTCAAGCGGCTTGCTGAGGAATTTGGTCCTGAATGGGCAATGCAACATATAGTTCCTCAG

upper sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
------gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatatt-gcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
          | ||| ||  | || |||  |  ||        | ||  | ||   ||||     |   |          || |   | |  |  || ||||| | || ||||| || || |||||||||||||| || |||||||| ||||||||||| ||||| ||||| ||||||||| ||||||| |||
tattttaagagggctttcatcatctttgtcatcgttttctttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG

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|192298924|gb|FG987669.1|FG987669
EST:     TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|9205515|gb|BE331739.1|BE331739
EST:     TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|6914739|gb|AW396269.1|AW396269
EST:     TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTTGAAACGCCTTGCTGA
genomic: TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAAC-TTGAAACGCCTTGCTGA
EST: gi|254327333|gb|GR836942.1|GR836942
EST:     TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|308098474|gb|HO760215.1|HO760215
EST:     TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
EST: gi|308098470|gb|HO760211.1|HO760211
EST:     TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAG                         GTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA
genomic: TTTTTGATGACAAACTTGGTGCTCTTTGCATGCAGTGGTTACAGGATAAGgtttgtgctc ... gttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG
                               tgttaac  putative branch site (score: 2)
                           tttttgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctctccacttccttgctagtgtgggtgcattttgggaactgcatattgcacatgactgtttttgttaacaaccttagttattgtagGTTCATTCAATTCGCGAAGCAGCTGCTAACAACTTGAAACGCCTTGCTGAAGAATTTGGACCTGAGTGGGCTATGCAGCACATAATTCCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA