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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgattactaaatgctactcatacttacatattttaaacttttttattgggcaagttagaaagatgcataatctaatcattttacttctgattgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG

Basic information

species Glycine max
transcript GLYMA11G21650.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g03510.t01 (Vitis vinifera), 3'ss of exon 2
---ttgattactaaatgctactcatacttacatattttaaacttttttattgggcaagttagaaagatgcataatctaatcattttacttctgat-tgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG
   |   || || | || |  || | |   |||   ||    || |||  ||||    || || |||||  |||| |   | |||| ||| || | |   ||||||  | ||||||||  | || || || ||||| |  ||||| | |||||||||||||||||| || ||||||||||||
gtatgattttctcactgattttcttccactcattcctt----ttcttttctgggtttttttgatagatgtttaatttt-cctttttccttttgttatatggcagGAAATGGAAGTAAATTTAATTATCACGGATTATTCCATGCCTGGAATGACTGGCTATGATCTCCTCAGAAAGATCAAG

upper sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0067g03490.t01 (Vitis vinifera), 3'ss of exon 3
---ttgattactaaatgctactcatacttacatattttaaacttttttattgggcaagttagaa-agatgcataatctaatcattttacttctgattgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG
   |   || || | || |  || |   | |||  |||     | ||| |||||    |||||| |||||  || | |  || |||| ||| |   |   ||||||    |||||||| || || || |||||||| |  ||||| | |||||||||||||||||| || ||||||||||||
gtatgattttctcactgattttcttctattcatccttt-----tcttttttgggggttttagaatagatgtttatttttttccttttcctttttgctatggcagGAAACGGAAGTAAATCTAATTATTACTGATTATTCCATGCCTGGAATGACTGGCTATGATCTCCTCAGAAAGATCAAG

upper sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
------------------------------------------------------------------------------------------ttgattactaaatgctactcatacttacatatttta---aacttttttattgggcaagttagaaagatgcataatctaatcattttacttctgatt--gctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG
                                                                                          ||  ||      |  |  |  |  |     ||  ||   ||  |  |  ||||   | ||           |  |    || | |  ||| || ||  | ||||||   |  || ||||| ||||||| || || || |||||||| |||||||| |||||||||||||| |  ||| |||||
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG

upper sequence: GLYMA11G21650.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ14701 (Selaginella moellendorffii), 3'ss of exon 2
ttgattacta-aatgctactcatacttacatattttaaacttttttattgggcaagttagaaagatgcataatctaatcattttacttctgattgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG
| | |   |    || |  |  |   | |    |       | |||    |      | || |  | | |    |  ||    |  | ||  ||| ||||||   |  || ||||| ||||||| || || || |||||||| |||||||| |||||||||||||| |  ||| |||||
tgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgctt-ttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG

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|58018386|gb|CX705128.1|CX705128
EST:     AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAG                         GATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
genomic: AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAGgtacaattct ... attgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
EST: gi|192334799|gb|FK025948.1|FK025948
EST:     AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAG                         GATGTAGAAGTAAACCTGATCATAACCGATTACTGTATGCCAGAAATGACT
genomic: AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAGgtacaattct ... attgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
EST: gi|7283519|gb|AW596125.1|AW596125
EST:     AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAG                         GATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
genomic: AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAGgtacaattct ... attgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
EST: gi|7795492|gb|AW780889.1|AW780889
EST:     AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAG                         GATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
genomic: AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAGgtacaattct ... attgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT
EST: gi|192334800|gb|FK025949.1|FK025949
EST:     AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAG                         GATGTAGAAGTAAACCTGATCATAACCGATTACTGTATGCCAGAAATGACT
genomic: AGAAGAGAAATGAGGAGCCTCCTCCCTGTATTGCTCTAGAATCCCATCAGgtacaattct ... attgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgggcaagttagaaagatgcataatctaatcattttacttctgattgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG
                                        ttctgat  putative branch site (score: 3)
                      ataatctaatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgattactaaatgctactcatacttacatattttaaacttttttattgggcaagttagaaagatgcataatctaatcattttacttctgattgctgcagGATGTAGAAGTAAACCTGATCATAACTGATTACTGTATGCCAGAAATGACTGGCTATGATCTGCTGAGAAAGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcataa