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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaatttttcatcatcttttttccttgataagtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT

Basic information

species Glycine max
transcript GLYMA13G38980.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g64490.1 (Oryza sativa), 3'ss of exon 11
gttgtggcccctatcttgcctgatatat-ttatgtatgtga-atgtgaaggcaatttttcatcatctttttt-ccttgataagtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
  | |      | |||| | |  | | |   |  |   ||   | |||    || || |||   |    ||   ||| |      ||  || | ||||||||||||||||| ||  | || || |||||||| || ||||| ||||||||||||||||| || || || |||||| |
--tatatttgttttcttccgtagtgtttaccaaattgatggtgtttgactcaaagttgtcaaagttcagttaatcttaagtttactcccatgt-ttgtttcagGATATGGCTGGACTAATTAGTAAGATAAATCGCTCCTCCATTGGCCCTTTGCCTCCATGCTACTCTCCATCTAT

upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 10
-gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaatttttcatcatcttttttccttgataagtgtcgtatatc-----ttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
   | |||  | |       ||  | |  |    | |   ||||  |   | |||| |  |   |||||    || |    | |  |  |||     |   | ||||||||||| || || ||||| ||||||||  | ||||| |||||||| |||||| ||||||| ||  | ||| |
aaatatggaacattggaattcttgtgtgct---atttaacaatgcta---ctatttgtatttgccttttaagtttcagtgatcttatgaatcaacaatacctgcagGATATGGCTGGATTAATAAGTAAGATAAATAGGTCCTCCATTGGCCCCTTGCCTGCCTGTTACTCTTCTTCTAT

upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 11
--gttgtggcccctatcttgcctgatatatttatgta-tgtgaatgtgaaggcaatttttcatcatcttttttccttgataagtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
   |  |  | |     |||| |  | || | ||||| ||| | |        || | |  |   |    |   |||||    |     || | |  |||||||||||||| ||  ||||||| |||||||| || ||||| ||||||||||||||| | |  |||||  ||||| |
atctcatctctcagcctttgcatattttact-atgtagtgttattaatttcaaaagtatagaagttgaggtaagcttga-gcttactccatgtttc-tttcagGATATGGCTGGACTGATAAGTAAGATAAATCGCTCCTCCATTGGCCCTTTGCCTACTTTCTATTCTTCATCTAT

upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G137118_T01 (Zea mays), 3'ss of exon 11
gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaatttttcatcatcttttttccttgataagtgtcgtatatc-ttgttt-cagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
  |  | ||  |  ||  | | ||||| | | || |  |         ||  |     |  |    |||    ||||  |    | || || |||  | ||||||||||| || || |||||||||||||| || || || || || ||||||||| ||||||| ||    ||| |
-cttggaccttttcctctcttaatataatgacgtgta-gtcctcccgcgcgttcgagaaaaaaaaatttctgatgatctgacctgaatttcattgcctgcagGATATGGCTGGATTAATAAGCAAGATAAATCGGTCTTCCATGGGTCCTTTGCCTGCCTGTTACTCAGTGTCTAT

upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 10
gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaatttttc---atcatcttttttccttgataagtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
    |  | |  |  ||    |||  | |  | |  ||     || |    || | |    |  ||||| |  | ||      | |  ||||| |  |||||||||||||||||| | ||||||||| | || || ||||| ||||| || |||||||| || ||||| ||||||||
---atatcactgaagttaatggatggagtattcttggttcccctgcatttgatctcttcaaagtatcttatggcatttgcttttatgttatatatgatttcagGATATGGCAGGGCTTATAAGCAAGGTTAATCGCTCCTCAATTGGTCCGTTGCCTCCGTGCTATTCACCATCTTT

upper sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 10
gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaattt--ttcatcatcttttttccttgata--agtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
    |       || ||   |  |          || |||||    |  |  |||  | |||  | ||| |    | | |   |  |  || |||| ||||||||||||||| || || ||||| || ||||||||||| |||||||| ||||||||  | || |||||||| |||||
----tatatgtgattttaatttgttatcacccaaatatgaattctgaaactgtttactccattttatttgtattctaacattggcattctacatctggtttcagGATATGGCTGGATTAATAAGTAAAATAAACCGTTCTTCTATTGGTCCTTTGCCCTCATGCTATTCCCCTTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggcaatttttcatcatcttttttccttgataagtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT
                         ccttgat  putative branch site (score: 5)
                                            tcttgtttc  putative PPT
     aatttttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtggcccctatcttgcctgatatatttatgtatgtgaatgtgaaggcaatttttcatcatcttttttccttgataagtgtcgtatatcttgtttcagGATATGGCAGGGTTGATAAGCAAGATAAACCGTTCCTCTATTGGCCCTTTGCCTCCCTGTTATTCCCCATCTTT

- - tggcccc
- - - - - - - - tgcctga
- - - - - - - - - - - - - - - -tgtatgt
- - - - - - - - - - - - - - - - - - - - - gtgaagg