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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG

Basic information

species Glycine max
transcript GLYMA08G20670.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgta---ctgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
      |  |||| ||  || | ||       |  || | |   |  |  ||   |  ||  | |   | |    |    |  | | | |   ||   | ||||||||||  |||||||||||||||||||||| |||   |||||||| || || || |||||||||||||| |||||  ||| ||| |||||||| || ||
accttctgaactacattctt-tattattttgctcttttttaatcttggacatcttacattctatatttcctgatccaagatacttaacttccatt--gtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 2
tatgattatactatatgattatcttgcaaaatttattatcagattatgggatga-catgttt---caaacagcgtactgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
  || |  |  |  |||  || | ||||       ||       | |||||    ||| | |    |   |  |   ||  |  | |   |||  |   | ||||||||||  ||||||| || ||||||||||| |||   |||||||| || || ||||| ||||||||||| ||||| ||||  || || || || || ||
agtgttccttttgcatg--tagcatgcattgcacttttctgctgtgtgggaccttcatatctgcatatttatagctttggatgctgactgttg--tggtttcagAATATGTGTTGCAAGAGATCACAAAAGCTGGTTTTGTGGAACCTACCCCTATCCAATCGCAAGGTTGGCCGATGGCATTGAGAGGCCGCGACCTTATTGG

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------tatgatta-tactatatgattatcttgcaaaatttat-tatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                                 | |||||| |   |  |   | ||||  |    | || || || ||       |   || |||  |    | ||||||| |     |||  | ||    |||| |||||  || ||||  |||  || ||||| |||||||||||||| || || |||||||| || ||||| |||||| ||||||| |||||||| || ||
gtaaactcttgaatttggcaatcatgtagagcttgtgattagtttcacttacatgtcttagatgtatgatgtagcatatatgcctgttttatttttggatatacctactgatatagtttcct--gattggctcagATTATGTTTTGGAAGAGGTTAAGAAGGCTGGTTTTACTGAACCTACGCCTATACAATCTCAGGGGTGGCCAATGGCTATGAAGGGACGTGATCTTATCGG

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
-tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggttt----aatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
  || | |  |||       | |||||  || ||     |  ||| ||||    | || ||  ||     ||  | ||| || |    |   ||    | ||||||||||||  |||||||||||||||||||||||||| |||||||||||||||| ||| ||||||| ||||| |||||||||||||| |||||| | || ||
aaatcagtg-actggcaacctttcttgagaagttatgctttggatgatgg----atattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S59_81V6.1 (Physcomitrella patens), 3'ss of exon 3
tatgattatactatatgattatcttgca--aaatttattatcag-attatgggat--gacatgtttcaaacagcgtactgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
       | ||| | |||||     | |       | ||    |    || || |  |    | |    ||   |    | || |        |   |    |||| ||||| ||||| ||  |    || || || || || || || ||| | |||||| | ||||| ||||||||||||||||||||||| ||  |||| ||
-----ggacactgtgtgattgatcgggatcggtcctgttggtggtggcattgggtttgtggcgctgatcacgctgcggcggttgtgtgtttgggaaatggagcagATTATGTGCTGCATGAGGTGCTGAAGGCAGGGTTCACGGAGCCAACAGCTATTCAAGCGCAAGGCTGGCCCATGGCTTTGAAGGGGCGCGACTTGATCGG

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10791 (Selaginella moellendorffii), 3'ss of exon 2
tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggtttaatc--cagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                                        ||   | ||  |    | |     |||  ||  |||||  ||     ||| |   |   |||| ||||| || || ||| ||   ||||| || || |  || || ||  |||||||| ||||||| ||||||||||||||||| ||| | |||||  ||||
--------------------------------------gtaggcgaaggtttcttctatcgaggacaaggttttgattgatcttatgtggatgttttggcagACTATGTTCTCCAGGAAGTTCTCAAAGCCGGTTTCAAGGAGCCCACCGCCATTCAAGCTCAAGGATGGCCCATGGCTTTGAAAGGGAGGGATCTAGTAGG

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ26152 (Selaginella moellendorffii), 3'ss of exon 2
tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggtt-taatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                                        ||   | ||  |    | |     |||  ||  |||||  ||     ||| | |  |||||| ||||| || || ||| ||   ||||| || || |  || || ||  |||||||| ||||||| ||||||||||||||||| ||| | |||||  ||||
--------------------------------------gtaggcgaaggtttcttctatcgaggacaaggttttgattgatcttatgtggatgttttccagACTATGTTCTCCAGGAAGTTCTCAAAGCCGGTTTCAAGGAGCCCACCGCCATTCAAGCTCAAGGATGGCCCATGGCTTTGAAAGGGAGGGATCTAGTAGG

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|151407052|gb|EV276867.1|EV276867
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|4288854|gb|AI441392.1|AI441392
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTG-TTTTCCAG                         AAT-TGTACTGCAAGAAAT-ACAAAAGCTGGCTT-ACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|7925520|gb|AW831546.1|AW831546
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATACGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|209700616|gb|BW670334.1|BW670334
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|213595546|gb|DB968510.1|DB968510
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|151397571|gb|EV267444.1|EV267444
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|9986238|gb|BE660346.1|BE660346
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
EST: gi|298192717|gb|HO033151.1|HO033151
EST:     GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAG                         AATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA
genomic: GCGAGATATCCCGAAACCTGTCAAGACCTTTCACGATGCTGGTTTTCCAGgtatttctgt ... tttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggatgacatgtttcaaacagcgtactgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG
                            tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggtttaatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - cttgcaa
- - - - - - - - - - - - - - - - - - - - - - - - - -tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaaaca