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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagttttggtcttttattcttggcctgatatattgctttggatgttgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG

Basic information

species Glycine max
transcript GLYMA03G27380.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g17170.1 (Oryza sativa), 3'ss of exon 1
ttcttatgatgttgtggtc--gtttgatgattaattctgctttatgcagttt-tggtcttttattcttggcctgatatattgctttggatgttgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG
    |  |  ||||  |||  | ||  || ||     | |     |||  |  ||| |  ||  |  ||  |   | | || ||||   | ||  | || |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||| ||| |||| |||||
---gttcgtagttgcagtctagcttcttgctttgcatttcaccgagcacctggtgggcgcttgctaatgctcctttttttttcttttttttttttt-ttgcagAAAACAAACCCAGTGGTGGCTGAGATCTTCTCGCTCATGTCCAGGGATGAGGCCCGGCACGCTGG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G56940.2 (Arabidopsis thaliana), 3'ss of exon 2
ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagttttggtcttttattcttggcctgatatattgctttggatgt--tgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG
  || || | || |  ||      |    | |  ||  ||  ||    |||||    || || ||||| |||| |      || ||| |  ||   || |||||||| |||||||| ||||||||||| ||||| || |||||||| |||||||| || ||||| ||
-gctcattaggtggaagttagagcacatgtgagacttgttgttgtttctttggatcatt-ttattggcttgattttgaatctttgatctgatggcattgcagAAAACAAACCCTGTTGTGGCTGAGATCTTCTCTCTTATGTCTAGAGATGAAGCAAGACATGCCGG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0040g00390.t01 (Vitis vinifera), 3'ss of exon 1
--ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagttttggtcttttattct--tggcctgatatattgctttggatgttgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG
  | || |     ||    |   || |   |     | | |||||   | | ||      |       || ||||||       | |     |||||  | ||||||||||| || ||||| |||||||||||||| || ||||| || ||||||||||||||||||||
aatgctaaaccctttccaattaattaaaactattgccagatttatatggatatgacaaactgggaaagtgacctgatgggcatttct----attgatactgcagAAAACCAATCCAGTGGTAGCTGAGATTTTCTCTCTTATGTCCAGAGATGAAGCCAGGCATGCTGG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S97_248V6.1 (Physcomitrella patens), 3'ss of exon 1
ttcttatgatgttgtgg-tcgtttgatgattaattctgctttatgcagttttggtcttttattcttggcctgat-atattgctttggatgttga-tgtta-cagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG-----------------------------------
        ||||||    ||   |  |    ||      || ||     ||   ||   |||  |||   || | | |||||||       ||| ||| | ||||| || |||||||||||||||||||||||| | || ||||| |||||||||||||| ||||||||                                   
----agaaatgttgccactccaattgttgcaaacagcttttgatctttcttctctccgatatgattgtaatgttgaaattgcttccttccatgaatgtgaacagAAGACAAACCCTGTGGTGGCTGAGATTTTCACCCTTATGTCAAGGGATGAAGCCAGACATGCTGGCTTCTTGAACAAGGGACTGTCAGACTTCAACTTGG

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S239_18V6.1 (Physcomitrella patens), 3'ss of exon 1
ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagtt-ttggtcttttattcttggcctgatatattgctttggatgttg-atgtta-cagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG-----------------------------------
| | | ||   |||| |  |  |  |     |||| | | | ||   |  ||      | |||||    | ||   | ||  || ||||||  |  | | ||||| ||||||||||| ||||||||||||||| |  ||||||| || || |||||||| ||||||||                                   
tccgtctgcc-ttgtag--ggctagtagcatattcgggtatttgtgttgattacgaactgattctaatacggaggaactgtctttgatgttttacctcatcagAAGACCAACCCTGTTGTGGCTGAGATTTTCACCTTGATGTCAAGAGACGAAGCCAGACATGCTGGGTTTCTGAACAAGGGACTGTCAGACTTCAATCTGT

upper sequence: GLYMA03G27380.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S239_18V6.2 (Physcomitrella patens), 3'ss of exon 1
ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagtt-ttggtcttttattcttggcctgatatattgctttggatgttg-atgtta-cagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG--------------------------------------
         ||   ||   |  |  |     |||| | | | ||   |  ||      | |||||    | ||   | ||  || ||||||  |  | | ||||| ||||||||||| ||||||||||||||| |  ||||||| || || |||||||| ||||||||                                      
------gtctgccttgtagggctagtagcatattcgggtatttgtgttgattacgaactgattctaatacggaggaactgtctttgatgttttacctcatcagaagACCAACCCTGTTGTGGCTGAGATTTTCACCTTGATGTCAAGAGACGAAGCCAGACATGCTGGGTTTCTGAACAAGGGACTGTCAGACTTCAATCTGTCTC

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|298169746|gb|HO021106.1|HO021106
EST:     CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|209726222|gb|BW659574.1|BW659574
EST:     CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|213600522|gb|DB960070.1|DB960070
EST:     CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|213595254|gb|DB963987.1|DB963987
EST:     CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|20813125|gb|BQ297603.1|BQ297603
EST:     CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCCGTGGTGGCTGAGATTTTCTCACTGATGTCTAAGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|151399052|gb|EV268923.1|EV268923
EST:     GGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: GGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|213605013|gb|DB956360.1|DB956360
EST:     CTGAATTCTCTGGCTTCCTTCTCTACNAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
EST: gi|209714176|gb|BW679505.1|BW679505
EST:     CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAG                         AAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA
genomic: CTGAATTCTCTGGCTTCCTTCTCTACAAAGAGCTTGGAAGGAGGCTAAAGgtatggtttc ... gatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttggtcttttattcttggcctgatatattgctttggatgttgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG
                                         tgttgat  putative branch site (score: 4)
          ttttattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcttatgatgttgtggtcgtttgatgattaattctgctttatgcagttttggtcttttattcttggcctgatatattgctttggatgttgatgttacagAAAACCAACCCTGTGGTGGCTGAGATTTTCTCACTGATGTCTAGGGATGAAGCCAGGCATGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - gttgtgg
- - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctttgg