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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA

Basic information

species Glycine max
transcript GLYMA20G25120.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os05g08990.1 (Oryza sativa), 3'ss of exon 17
---------------------------------------------------------tgtattgttaagctttatcatggtattaccacttcat-atgatgttggtaggcttatgtttgtatgcttctgattttatgttgtta-tgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
                                                           ||  |     ||||      | | | |  ||  |  || |      | |    || |  ||      ||  | | ||  ||  | ||   |  | | ||| ||||||| || |    ||| || || || || || || || ||  |  | |||||||||||||||||||| ||||||||||| ||| | ||  |||| |
gtaattcttatgtctgaatgacttaatcattttgagaattaaaaatctggtttagtggttacagagtccctttggttctgcacttctgctcaaagattagacacattgagcaatataagttcatcacttctctgattctggaactgtggtcatccctagGTTCCATTCTCAAGAACTGTCTACATCGAGCAGTCTGATTTTCGTGTAAAGGATTCAAAAGATTATTATGGGCTTGCTCCTGGTAAAACAGTACTACTAA

upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: AT1G25350.2 (Arabidopsis thaliana), 3'ss of exon 17
tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
                     |  |     | |||  |  ||  | ||   ||  |      ||  | ||| |||  || | || |    | ||   ||| | || || || |  |||||||| ||||| || || |||||||| ||| | |||||||||||||||||||| || || ||||| ||||||||  | || |
---------------------gtaagctgtatttcgca-aatacttgttttctactaacaacatattactg-tttcttgatattttttcctggt--ctagGTACCGTTCTCTAGAGTTGTATACATTGACCAATCTGACTTCCGAATGAAGGATTCAAAAGATTATTATGGGCTCGCCCCTGGTAAATCTGTTTTGCTAA

upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv01s0011g03740.t01 (Vitis vinifera), 3'ss of exon 18
---tgtattgttaagctttatcatggtattacc--acttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
   |  | | || | |  |||  || | | | |  |  ||| ||  || || |||  ||   ||| |  |    |||||||   || || | |  ||    |||| |||||||||| ||| |||| || ||||| ||  | || || |||||| ||||||| |||||||| ||||| ||||||||||| ||||||||  | ||||
ttttccaattttgatcactatactgttctgatcctatatcaaatattgctgttagtgttggatttctgag----tgattttgcatttttctcccctt-cctttagGTTCCATTTTCTAATATTGTGTACATTGAGCACACTGATTTTCGGATGAAAGATTCGAAAGATTACTATGGGCTTGCTCCTGGTAAATCTGTCCTGCTCA

upper sequence: GLYMA20G25120.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv15s0021g01230.t01 (Vitis vinifera), 3'ss of exon 18
---tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgt-ttgtatgcttctgat--tttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
      | |         || |||    | || |  | |    || ||   || |||   | || ||  ||    ||  ||| | || |  ||  ||  || |||| | || ||||||||  ||||||| ||||| || || || || |||||| | ||||||||||| || ||||| ||||||||||| ||||| ||  ||||||
tggcaaagtagaggaacctaccat----taactatgtaactccatattca-agacttggatgttttaaactgtcaataatttttcttttgctgttttcatt-ttagGTGCCCTTTTCCAAAATTGTATACATTGAGCAGTCTGATTTTCGGATGAAGGATTCAAAAGACTACTATGGGCTTGCTCCTGGAAAATCCGTCCTACTCA

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|33389687|gb|CA852894.1|CA852894
EST:     CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG                         ATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
genomic: CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAGgtgaaattga ... ttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
EST: gi|14999379|gb|BI320344.1|BI320344
EST:     CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG                         ATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
genomic: CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAGgtgaaattga ... ttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
EST: gi|5753691|gb|AI960978.1|AI960978
EST:     CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAG                         ATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA
genomic: CAAAGAAATGGCCTGATGCTCAAGCTGATGATGCTTCTGCTTTCTACAAGgtgaaattga ... ttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA
                     ttctgat  putative branch site (score: 3)
                                            tttgttctt  putative PPT
                          attttatgttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtattgttaagctttatcatggtattaccacttcatatgatgttggtaggcttatgtttgtatgcttctgattttatgttgttatgcatttgttcttagATTCCATTTTCCAATGTTGTATATATTGAACATTCGGACTTCCGGATGCAAGATTCAAAAGATTATTATGGCCTTGCTCCTGGGAAATCTGTGATACTCA

- - - - - - - - - - - - - - ccacttc
- - - - - - - - - - - - - - - - - - - -gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcat