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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcaaaagtttaaatttgtgaaagacaaatgtgatttacacatgtcttcaaaagaagcagttgaggagagaatgcaacacccactatgttttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC

Basic information

species Glycine max
transcript GLYMA06G13640.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G13640.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g35810.1 (Oryza sativa), 3'ss of exon 1
agcaaaagtttaaatttgtgaaagaca---aatgtgatttacacatgtcttcaaaagaagcag---ttgaggagagaatgcaacacccactatgttttccttgc-agAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC
        | |||| |  |   || |    |  || ||||   | | |||||||  |    |    ||    | | ||    | ||||  | || | |  |||  ||||| | || ||| |||| || ||||| ||  | || |||||||| ||||| || ||||||||||||||||||||||| || ||||| || ||| | ||||
------cttctaaactcattctagcctcccagagttattttt-cttttcttcaatggctttatgtcttcctaaaataacatcataccctgtttgctctggttgttagAGGTTGCCTCCACTGTCCACAGAGCCAAACAGATGCGAGCGTGCTTTTGTCGGGAACACAATTGGTCAGGCAAATGGGGTGTATGACAAGCCACTCGATC

upper sequence: GLYMA06G13640.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G53490.3 (Arabidopsis thaliana), 3'ss of exon 2
agcaaaagtttaaatttgtgaaagacaaa-tgtgatttacacatgtcttcaaaagaagcagt---tgaggagagaatgcaac--acccactatgttttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC
        | | |  || |      |    | |  | ||    ||| |   ||    ||  |   | || |   || | ||   |   |     | ||  || ||||| ||||| || || ||||| || ||  | || |||||    ||||||||||| ||||| || ||||| ||||||||||| ||||| |||||| | ||||
-----gtctgtcacattatatggccctttctcttttctatgtttgtgtctgaagatggctatgttttagaatttaaagaaatggataaatggattgtttttttcagAGACTTCCTCCGTTATCAACAGAACCAGACCGGTGTGAAAAAGCATTTGTTGGTAACACGATAGGTCAAGCAAATGGTGTCTATGACAAACCACTGGATC

upper sequence: GLYMA06G13640.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0098g01540.t01 (Vitis vinifera), 3'ss of exon 2
agcaaaagtttaaatttgtgaaagacaaatgtgatttacacatgtcttcaaaagaagcagttgaggagagaatgcaacacccactatgttttcct-----tgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC
        | |  | |  |  | |     | | | | |   || |||   |  |  || | ||| ||     |  |      |  ||||| || |     |||||||||| || |||||||| || || ||||| ||||||||||| ||||||||||| ||||| || ||||| |||||||| || ||||| || ||| | || |
-----ttttcttcagtcatccatgttctttctaactaatttatttctgttactgctgctgctgatgatgatgtctatatattatgatgttgtcttatgtttgcagAGGCTGCCTCCATTGTCCACAGAACCCAACCGCTGTGAGCGGGCATTTGTTGGAAACACGATCGGTCAAGCAAATGGCGTTTATGACAAGCCAATCGACC

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|5607156|gb|AI901254.1|AI901254
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|298171589|gb|HO021181.1|HO021181
EST:     CAGCTTGAGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|58021910|gb|CX708651.1|CX708651
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|151398004|gb|EV267882.1|EV267882
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|13562703|gb|BG550923.1|BG550923
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTACCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|192321720|gb|FK013602.1|FK013602
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|120532686|gb|EH260819.1|EH260819
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
EST: gi|192320229|gb|FK012675.1|FK012675
EST:     CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAG                         AGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT
genomic: CAGCTTGTGCTGTTACTTCTGCTGCATTTCCTGTTACTGCTGCTACTCAGgttttaattg ... ttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaaaagaagcagttgaggagagaatgcaacacccactatgttttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC
                                         tgttttcctt  CT-rich tract
                                       tatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcaaaagtttaaatttgtgaaagacaaatgtgatttacacatgtcttcaaaagaagcagttgaggagagaatgcaacacccactatgttttccttgcagAGGCTTCCCCCATTGTCAACTGAGCCCAATCGCTGTGAGCGTGCATTTGTTGGCAACACAATTGGTCAGGCAAATGGTGTATATGATAAACCATTAGATC

- - - - - - - - - -gaaagac
- - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacacc