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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaattgaaatcgagctttgttattgacgcgattacctgaaaatcctgtttctgataatggtgtttccatttccatgcttatatccgtgtgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG

Basic information

species Glycine max
transcript GLYMA03G40000.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 1
-attaattgaaatcgagctttgttattgacgcgattacctg-aaaatcctgtttctgataatggtgtttccatttccatgcttatatccgtgtgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG
  | | |     | | ||    || ||       | |  ||    | | |     ||  ||  |  |||| |||||  |  |  | |  || ||   | |||||||| ||||| || |||||||| ||||| ||||| |||||||||||  | |  || ||  | || || |||||| || ||||||| || |||||||||
tctgagtgcgccttgcgcccatttttttttttcttcatgtgcgctaactttaacttggcaactgattttcgatttctgt-ttcctgtatgtatggctc-cagAGGGACGACATGGAGGTGCTTGACGAGCCTCTCTACGCAAATTTCCTGCGTGCCACAGGCGTCGACAGGCCCTACCGGCAGGAGCTCCTGTCCAAAATG

upper sequence: GLYMA03G40000.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 11
attaattgaaatcgagctttgttattgacgc--gattacctgaaaatcctgtttctgataatggtgtttccatttccatgcttata-tccgtgtgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG
   | |||||  |    |||||   ||   |    ||||||  |||     || ||  |  |    |||   |     || || |  |  ||||  | | |||||||||||  | |||||||||||||| ||||||||||||||||| ||| | ||||| ||| |||| || |||||| | |||||||| || ||||| |||
---acttgaagccattatttgtgcatgtttctgagttacctctaaaattaattcctcctcgttaattttatgtccttttggttgtgctttgtgttttcctcagAGGGATGATTTTGAAGTGCTTGATGAACCCCTCTATGCAAATTTTCTTCGGGTAACAGGTGTTGAAAGGCCCTACCGTGAGGAGCTTCTGTCCAAGATG
















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|298180727|gb|HO022166.1|HO022166
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
EST: gi|213615160|gb|DB964968.1|DB964968
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
EST: gi|192301788|gb|FG997674.1|FG997674
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
EST: gi|213614510|gb|DB969115.1|DB969115
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
EST: gi|46492660|gb|CN472216.1|CN472216
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
EST: gi|298170197|gb|HO018821.1|HO018821
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
EST: gi|151396136|gb|EV266013.1|EV266013
EST:     GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTCTTCTCAG                         AGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA
genomic: GGTCTGCTCCAAGATCCCTCAGTACTAGTCTCATGTATTCTTTTTCTCAGgtattgtacc ... tgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgtttctgataatggtgtttccatttccatgcttatatccgtgtgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG
     ttctgat  putative branch site (score: 3)
                                  ttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaattgaaatcgagctttgttattgacgcgattacctgaaaatcctgtttctgataatggtgtttccatttccatgcttatatccgtgtgctacacagAGGGATGACATAGAAGTGCTTGATGAGCCCCTCTATGCAAATTTCCTTAGAGTAACTGGTCTTGATAGACCCTACAGGGAGGAGCTACTCTCCAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - gtttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttat