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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

Basic information

species Glycine max
transcript GLYMA20G38030.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g21660.1 (Oryza sativa), 3'ss of exon 5
gtttcctctatttcacttgcaca----ctaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
   || |  |  ||   || | |    || |   ||  ||  |||   ||  |   | |  ||  | ||  |||||  |     |    |||    | || |||| | | ||||| || ||||||| |||||||||||| |||||||| || || ||||| ||  | |||||||||||||| || |||||||||||||||||||
--atctttgagctcctctgaaaagtttcttagtgctacatgatttgcctttttttttatgtac--gattgagattaatactggtttctttgtggactcgtgcagAAGCTTATTGGTGAGGGAGCAAGACTTGTTCGTGATGCCTTTCAGCTTGCTAAAGAGAAAGCCCCATGCATTATTTTCATTGATGAAATTGATGCAATTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 5
-gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
         |  ||   |       |  |   |||  |   | ||||  | | ||| |  ||    | |||    || |       ||  | || || ||||||||||| || ||||| ||||| ||||| ||||| |||||||| || ||||| || || || || ||||| |||||||| ||||||||||| |||||||
gaagaatattgctttggtccagtgttggtctattttcttcctttattggttcttct-gcttgctgctagatacatattaatgtctatgcgaattggtccagATGTTCATCGGTGATGGTGCAAAGCTTGTCCGTGATGCCTTTCAGCTTGCAAAGGAGAAATCCCCCTGCATCATTTTTATTGATGAAATTGACGCAATTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
   |     |  |    |  ||   | ||  |||  | ||  |  |   |  | ||   ||          | | | |  |    |  | || |||| |||||||||| |||||||||||||||||||| ||||| || || |  || |||||||| || || || || ||||| || |||||||| ||||| ||||| |
--gtatgaaaactagagtaaacgtaactgattttgatcttgttcctgtgatatttt--ttgaaccaaacggaaagtaactttttttagacttatgtatagATGTTCATCGGAGATGGAGCAAAACTTGTCCGTGATGCTTTCCTGCTTGCAAAAGAGAAATCCCCTTGTATTATATTCATAGATGAGATTGACGCAATAG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------------------------------------------------------gtttcctctatttcacttgcacact--aatgcctt-----tattgtttatattcatacctcttgactgggttttgattagaatgatctaacc-----tgtaattt-tgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
                                                                  ||| | || | |   |   | | |  | ||   |      | |  ||| ||        ||  | ||    ||||||  |||||  | |       |  ||||| | ||||||||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||| ||  | || |||||||| || ||||||||||| ||||| ||||
gtatatatatatatatatatatatatatatatgagtatcagattcaattctcatctcttagaactctttaccctgtctggatataagattttagtgttctggcaacaataattacatgtgacgagctataatgatacttgattgtaatgacatgatgacatatccaatttatatacagATGTTCATTGGAGACGGAGCAAAGCTTGTCCGTGATGCCTTTCAACTTGCCAAAGAGAAAGCTCCGTGCATTATCTTCATAGATGAAATCGATGCCATTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 5
gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttga-ctgggttttgattaga-atgatctaac--ctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
   | ||||| ||  | || |    |||    ||| |||  || |    |    |||| ||    ||| |||| |  | | | |||  ||   | | | | |||||||||||||| ||||| || |||||||| ||||| |||||||| || || ||||| || || || ||||| ||||||||||||||||||||||| || |
-aattctctagttgccatgta--gcaattatgttagtgtg-atgtgtgcattctttgatctattcttttattaaatgtaaccaaacaacttggaatgtattcagATGTTCATTGGGGATGGGGCGAAACTTGTCCGTGATGCCTTTCAGCTTGCTAAAGAGAAATCTCCTTGCATCATTTTTATAGATGAAATTGATGCCATAG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S218_133V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------gtttcctctatttcacttgcacactaatgcctttattgt-----ttatattcatacctc------ttgactgggttttgattagaatgatc--taacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
                                                  ||||  || ||| |    ||     |     | | |||     || | || | |  |       || ||| || |  | | |      |   |  |||     |   | |||||||||||||||||||| |||||||||||  | ||||| |||||  | || ||||||||| | || || || ||||| || |||||  | ||||| ||||
gttttgtcctgctctctccttagtgttttcttctggactggattttgtattttcagctttttgagaaacatgtacagaatctcactgtagaacttgttttaagaagttgggtcattcacttggctaagctcaaggcccttgttctcctcctgatcgttgcagATGTTCATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTTCAGTTGGCGAAAGAAAAGGCTCCTTGTATCATTTTCATTGATGAGGTGGATGCTATTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S340_7V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------------------------------------------------gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattaga-atgatctaacctgtaattttgt-acagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
                                                                              | || | || || | ||   ||    ||   | ||  | |  ||| || |   |  |  || | || |||    |  |  || ||||  |  |  | ||||||||| ||||||||||| |||||||||||  | ||||| || || |||||||| |||||  | || || || || || || |||||| | ||||||||||
gtgatttcttggttttacttgtttatctatggactctcgtcagttctggtttaggatgttgttttgccttaacgcctttgtcatttacttaatttttccatgggtggagtcatcttgttcatttatcctggtcaa--ggctcttcattgactacaagatatcctgatacgtaatcacagATGTTTATTGGAGATGGTGCAAAACTTGTGAGGGACGCGTTCCAGCTAGCAAAGGAAAAAGCTCCCTGTATCATCTTCATTGATGAAGTAGATGCAATTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 5
gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
                                      | | | |    ||   ||  |||   |  | ||   |   || | | | |  ||     ||||||||||| |||||||||||||| || ||  | || |||||||| || |||||||| ||| | || ||||| ||||| || |||||| | || || ||||
------------------------------------gttctgtgtaggaactctttacctg---tcgggttcttaaactcaagcttctggttcgtcgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

upper sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 5
gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
                                      | | | |    ||   ||  |||   |  | ||   |   || | | | |  ||   | ||||||||||| |||||||||||||| || ||  | || |||||||| || |||||||| ||| | || ||||| ||||| || |||||| | || || ||||
------------------------------------gttctgtgtaggaactctttacctg---tcgggttgttaaactcaagcttcttgttcgttgcagATGTTCATCGGAGATGGAGCAAAGCTCGTAAGAGATGCCTTTCAGCTGGCAAAAGAGAAGGCGCCCTGCATCATTTTCATCGATGAAGTCGACGCTATTG

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|298189083|gb|HO037486.1|HO037486
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
EST: gi|208108713|gb|GD907145.1|GD907145
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAA
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAA
EST: gi|193427383|gb|FK394837.1|FK394837
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGG
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGG
EST: gi|7233106|gb|AW568456.1|AW568456
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
EST: gi|192327046|gb|FK015213.1|FK015213
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
EST: gi|192317514|gb|FK008966.1|FK008966
EST:     CCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
genomic: CCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
EST: gi|208084369|gb|GD882317.1|GD882317
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTC
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTC
EST: gi|298174321|gb|HO017657.1|HO017657
EST:     CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAG                         ATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA
genomic: CACAGACAAATGCCACTTTTCTGAAATTGGCTGGCCCTCAACTGGTCCAGgtatgacaat ... ttttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG
                                atctaac  putative branch site (score: 2)
                                          taattttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttcctctatttcacttgcacactaatgcctttattgtttatattcatacctcttgactgggttttgattagaatgatctaacctgtaattttgtacagATGTTCATTGGAGATGGAGCAAAACTTGTTCGTGACGCCTTTCAACTAGCAAAAGAAAAGTCACCATGCATTATTTTTATAGATGAAATTGATGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA