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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattccttttgtcacatttccaactgattgtttgttctttgacaaattataggcttcacggtttcacccttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG

Basic information

species Glycine max
transcript GLYMA04G02530.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 1
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 1
--tattccttttgtcacatttccaactgattgtttgttctttgacaaattataggcttcacggtttcaccc-ttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG
  |     || |  | ||||||||  | | ||| | |     || || |||    ||    |  |  || | ||||    || |   |||    ||| || |||| |||||||| || |||||||||||||||||||| |||||||| || ||||| ||||| || ||  |||| ||||||||||| ||||
ctttggagttattcctcatttcca--taactgtatttggggagaaaagttactaactatgtgtgtcaacacattcttctgttctcaatgttgaccaa-aacagGATTATGTGCCAACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTG

upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 2
-tattccttttgtcacatttccaactgattgtttgttctttgacaaattataggcttcacggtttcacccttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG
    | ||      | || |         ||| |    ||    ||| | |  | | | |     |    ||    |   |  |   ||      |   |||| || || || ||||| |||||||||||||| || ||||| ||||| ||||||| ||| || || || ||||| ||||||||||| |
ggcgtactgcaaggagatgtgttgtgcgatgtctcccattcactaaagtctctggtcc-cttcaacgatttttaaagcacagataattggtcgttttgcagGATTACGTACCAACCGTGTTTGACAATTTCAGCGCAAATGTCGTGGTCGATGGAAACACAGTCAATCTCGGATTATGGGATACAGCAG

upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 3'ss of exon 1
---tattccttttgtcacatttccaactgattgtttgttctttgacaaattataggcttcacggtttcacccttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG
    ||  |         |  |  |  | |        ||| | | | |        |  ||  || |    | ||  |   |||   ||  ||   |   |||| || || || ||||| |||||||| ||||| || ||||| ||||| |||||||  ||||| ||||| || || ||||||||||| |
agggatggcgcgcaagg-agatgtactttaccacagcgtctgttagacagcgcttcttgtactcttacgatgtcctaagcacatgcccgttcgtt--tcgcagGATTACGTTCCTACCGTGTTTGACAACTTCAGCGCAAATGTAGTGGTCGATGGAAATACCGTCAACCTCGGGTTATGGGATACAGCAG

upper sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 1
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 3'ss of exon 1
-----tattccttttgtcacatttccaactgattgtttgttctttgacaaat-tataggcttcacggtttcacccttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG
     | |    | | | | || |  |  |   | | | | ||||    | | | ||   ||  | |  | ||   ||     |||  |   | | |       |||| || || || ||||||||||| || ||||| || ||||| || || ||||||| ||| |||||||| ||| | ||||||||||| |
aacgctgtgatgtatat-atatatatatatatatatatatccttttcttattatttaatttttcctgggtgacatctcaagagtta-atccttattttg----cagGATTACGTTCCTACCGTTTTTGATAACTTCAGCGCGAATGTCGTTGTCGATGGAAACACTGTAAACCTTGGACTATGGGATACAGCAG

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|14258618|gb|BG881526.1|BG881526
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
EST: gi|208228807|gb|GE024227.1|GE024227
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTATGTGCCCACCGT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGT
EST: gi|207827775|gb|GD800368.1|GD800368
EST:     CACTTTTCCCACG                         GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
genomic: CACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
EST: gi|9563948|gb|BE473457.1|BE473457
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
EST: gi|207836636|gb|GD806633.1|GD806633
EST:     CACTTTTCCCACG                         GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTTGGTGGA
genomic: CACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGG-TGGTGGA
EST: gi|37996148|gb|CF807737.1|CF807737
EST:     TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
genomic: TCGGCAAAACCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
EST: gi|15288013|gb|BI471904.1|BI471904
EST:     CCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACG                         GACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT
genomic: CCTGCTTGTTGATTTCCTACACCAGCAACACTTTTCCCACGgtttctttct ... tcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attataggcttcacggtttcacccttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG
                               tttatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattccttttgtcacatttccaactgattgtttgttctttgacaaattataggcttcacggtttcacccttctctgtttatgtttgtgtgtcaataatagGACTATGTGCCCACCGTTTTTGACAATTTCAGTGCTAATGTGGTGGTGGATGGAAGCACCGTAAACCTAGGATTGTGGGATACAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - -tgtcaca
- - - - - - - - - tccaact
- - - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - gcttcac