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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgactctttttcttgttcattgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG

Basic information

species Glycine max
transcript GLYMA06G42830.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g14110.1 (Oryza sativa), 3'ss of exon 5
ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgactctttttcttgttcattgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
               ||     |   |||| || ||| ||||  | ||  ||||         |||   | |     ||  |  |||||  | ||  |||   |||  ||||||||| ||||||||||||||||| ||||| ||||| || |||||||||||||||||||| || || ||    || || ||||| ||||
--------------gtagcagaagtgaaaaggactggctttt--tgttggtgttatcaccaacgacagatatcacattt--tccttatgtgttttgacagATAAAGAATCATTTCCCATTCTTTGACATGGCATACCAAGGATTTGCCAGCGGTGATCCAGAGAGAGATGCTAAGGCAATCCGAATCTTCCTTGAAGATG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g35540.1 (Oryza sativa), 3'ss of exon 5
ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgactctttttcttgttc-attgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
                  | | ||     |  ||||    | || |||     |   ||| ||| |  || |  | |||| ||| |  ||||   || ||||  |||   ||||| || ||||| ||||||||||| ||||| ||||||||||||||||||||||||||||| || || ||    || |||||||| ||||
----------------gtatagaaaggtgacaattgtcaatggtcatttgctatattgtttttgccagttatagtagttctattttcttgatgcctttcagGTGAAGAAACATTTTCCATTCTTCGACATGGCATACCAAGGATTTGCTAGTGGTGATCCAGAGAGAGATGCCAAGGCAATTCGAATATTTCTTGAAGATG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G146677_T01 (Zea mays), 3'ss of exon 5
ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgactctttttcttgttcattgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
          ||||   |||  |||     |      |  ||||  ||| |||     | |  | | |   | |  | |     |  || |  | |  |||  ||    ||||| || ||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| || || ||    ||||| ||||| ||||
---------gtaatgggaactgaactggggaacaaaaaagttgtatttcctgtgatcctacaagccacacctaccagatttcactcttgttcctctatagGTGAAAAAACATTTTCCATTCTTTGACATGGCATACCAAGGGTTTGCCAGTGGTGATCCAGAGAGAGATGCCAAGGCAATCCGAATTTTCCTTGAAGATG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G30970.2 (Arabidopsis thaliana), 3'ss of exon 6
-ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgact--ctttttcttgttcattgttatgattgt-ttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
 | | ||    | |  |    |||   |       ||  | |  ||    || ||||  | |||||    |  | |   |   |   |   | |    || ||||||||    |||||| | ||||| || ||||| || ||||||||||||||||| ||||||| ||||||||| ||  |||| | ||| |||||||| ||||
gtgataactcatcagtttcttatagttat-----ctgtctatcattgactttatttc--tccttgatcagccctctgcagactaacatcgagttctcatttcagGCTAAAAAGCATTTCGCATTCTTCGATATGGCTTACCAAGGTTTTGCTAGTGGAGATCCAGCGAGAGATGCCAAGTCCATCAGGATCTTTCTTGAAGATG

upper sequence: GLYMA06G42830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0028g01820.t01 (Vitis vinifera), 3'ss of exon 5
ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgactctttttcttgttcattgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
                     ||  || | |   ||  || | || ||   |||     |  ||||| |   | || |      |||||||  ||| ||||  || ||||||||  | |||||||||||||||||||||||||||||||||||||| |||||||| ||||| ||  |||| |||||||| ||||| ||||
--------------------gtagacatagaagatg--ttcttttttttcagttctctgtactgactttccatgttttaatacattatgatcattttcagGTCAAAGGTCATTTTGCCTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGACCCAGAGAGGGATGCCAAGTCCATCAAGATTTTCCTTGAAGATG

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|19269530|gb|BM885786.1|BM885786
EST:     GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAG                         GCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
genomic: GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAGgtaacaattt ... ttgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
EST: gi|6913336|gb|AW394866.1|AW394866
EST:     GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAG                         GCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
genomic: GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAGgtaacaattt ... ttgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
EST: gi|254320419|gb|GR826868.1|GR826868
EST:     GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAG                         GCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
genomic: GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAGgtaacaattt ... ttgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
EST: gi|254340271|gb|GR858396.1|GR858396
EST:     GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAG                         GCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
genomic: GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAGgtaacaattt ... ttgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
EST: gi|13479298|gb|BG508641.1|BG508641
EST:     GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAG                         GCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT
genomic: GAGTAGATCCTTCAGAAGAACAATGGAGAGAGATCTCTTCCCAGATAAAGgtaacaattt ... ttgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttgtttcagttcttgactctttttcttgttcattgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG
              tcttgac  putative branch site (score: 3)
                                             ttgtttcc  putative PPT
                       tttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttacaaactttaatctaaacataaccaaaaagattggattttgttattcttgtttcagttcttgactctttttcttgttcattgttatgattgtttccagGCTAAGGGTCATTTCCCTTTCTTTGACATGGCATATCAAGGTTTTGCTAGTGGTGATCCAGAGAGAGATGCAAAAGCCATAAAGATTTTTCTTGAGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - ctaaaca
- - - - - - - - - - - - - aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg