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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattgttttggcaaactttttatgcatgggttctcttaatgagtaatgacttcatacaacgcacttttatattttcattattttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC

Basic information

species Glycine max
transcript GLYMA08G42730.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 3'ss of exon 11
taattgttttggcaaactttttatgcatgggt----tctcttaatgagtaatgacttcatacaacgcacttttatattttcattattttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
|     || || | || ||  |  |   || |      || |  |     ||||   ||  ||  ||| |   ||||||     || ||      || ||||||| |||||||| || ||||||||||||||| |  || ||||  ||||||| ||||| ||||| || |||||||   |||||||||| ||||| ||||||||
tgtggtttctgtctaatttggttcgttaggttattgcatccttcttttccatgatcacaatcatggcaatcgcatatttg----atattccccacatctttcagGAGGACCAACAGCAGAAACACGTGGAATTCTGGACCTGAGTGTTCAGTATTGGACAAGTCGAGGATGGGCATATCTTGATGTTAACTATGGGGGAAGCAC

upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g11190.1 (Oryza sativa), 3'ss of exon 11
--taattgttttggcaaactttttatgcatgggttctcttaatgagtaatgacttcatacaacgcacttttatattttcatt-attttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
   ||||| |  || |||         |||          ||       |   || | | || | |  |  | | |   ||| |  |||||  |||  || ||||||||| || | |||| |||||||| || |  |  |  |  ||||||||||||| || || || |||||||| ||||||||||| ||||| ||||||||
ttgaattgctaagggaaagca---gaacattaaaataaggaaatgtacttttttttaaagaaaggaaatggaaactcgtattgacattgttgcaattctttagGTGGACCTACAGATGAAGCACGTGGAGTTCTGGATCTTGGTGTTCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCAC

upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G120302_T02 (Zea mays), 3'ss of exon 11
------------------------------------------------------------------------------------taattgttttggcaaacttttta----tgcatgggttctcttaa-tgagtaatgacttcatacaacgcacttttatatt-ttcattattttg---tttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
                                                                                    ||| |||| |   | | |||  |    |  |||  || |  ||| |  ||    | ||| | |    ||  |  | ||     | |  ||||    |  ||  ||||||| |||||||||||||||||||||| |||| |  || | ||  | ||||| ||||| ||| | || |||||||  || ||||| || ||||| ||||||||
gtaagtgaattattcaaaccttatgttgcttgaaataattattcggtttgatccccctcaaaagaactatacatgtattcagcttaagtgttctcttagattttacaaaaataaatgatttttgctaagtaggtttgaaattctttcttttcagatgaaaatcacagaatgctttgacactctaaattttcagGAGGACCAACTGCTGAAACACGTGCAATTCTGGACCTCAGTGTCCAGTATTGGACAAGTAGAGGGTGGGCATATGTCGATGTCAACTATGGAGGAAGCAC

upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G000231_T01 (Zea mays), 3'ss of exon 9
taattgttttgg-caaactttttatgcatgggttctcttaatgagtaatga-cttcatac-aacgcacttttatattttcattattttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
   |  |||||| | |  |  || |  |  |  || | || |||  |||   ||| | |  |    |  ||||||  ||| ||||      | | | ||| ||||||||| || | |||| |||| ||  || |  |  | ||  | ||||||||||| || || || |||||||| ||||||||||| ||||| |||||| |
--ttgattttggtccagatgcttgtcaaaagcatcacatagtgaaaaatcttcttaacattattataagtttatagcttctttataccacatcattgttt-agGTGGACCCACAGATGAAGCACGAGGGGTTCTGGATCTTAGTGTGCAGTACTGGACAAGCCGAGGATGGGCATTTGTTGATGTTAACTATGGGGGAAGCTC

upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G36210.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------------------------------taattgttttgg---caaacttt----ttatgcatgggttctcttaatga-gtaatgacttcatacaacgcacttttatattttcattattttgtttgaatattt-------cagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
                                                                  |  |  | ||     ||   |||    | | | |||   | |     | |  |||  | | ||  || |      |   |  |  || |||||  ||||  || |       |||| ||||| ||||||||| ||||||||   |||||  |||  || || |||||||| ||||| ||||||||||| |||||||| |||||||||||||||||
gtatgttaaacttacgacatcccgatttttcaaaacttaatcaaaataattcctcagtttcagtcttgttcatcttaagatcatgttttcgtttcaagtatgtactttagctgtaacataaatattgcaatcagctatgcatggcacatcgatcatttttgttgacaatctgaatctacagGAGGACCTACTGCTGAATCACGTGGATCCTTAAATCTGAATATCCAATACTGGACAAGTCGAGGTTGGGCATTTGTTGATGTCAATTATGGTGGAAGCAC

upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 3'ss of exon 11
taattgttttggcaaactttttatgcatgggttctcttaatgagtaatgacttcatacaacgcacttttatattttcat-tattttgtttgaa-tatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
 ||      ||   | |||  ||| |||    |    | |  ||  |  | ||| |  ||       ||    |  ||| | |  ||| |||| |||| |||| || || ||   ||||||||||||||||||||| ||||| || ||||| ||||||||||| ||||||||||| || ||||| |||||||||||||||||
aaagatccatgattagctt--tatacattctctgaaatgaaaaggtagaatttcttctaatattgaattgggatagcatatgtgatgtgtgaaatattgcagGAGGGCCTACAAGTGAAACACGTGGAATTTTAAATTTGAGTATCCAGTATTGGACTAGTCGAGGTTGGGCATTTGTGGATGTGAATTATGGTGGAAGCAC

upper sequence: GLYMA08G42730.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 3'ss of exon 11
taattgttttggcaaactttttatgcatgggttctcttaa-tgagtaatgacttcatacaacgcacttttatattttcattattt-tgtttga-atatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
||||  |  | |   | ||| | |  |    ||||||||| |||  | | | || || | |  || |    |  |     |||   ||| ||| ||| | |||| || || || | |||| | |    ||  ||||| ||||| || ||||||||||| ||||| ||||||||||| || ||||| |||||||||||||||||
taatcatgatagatgattttctctatacc--ttctcttaaatgaacagtaaatt-attctatacattgaacttgtaatggtatacatgtgtgatatactgcagGAGGGCCGACCGATGAAGCGCACCAAAGCTTAAATTTGAGTATCCAGTACTGGACAAGTCGAGGTTGGGCATTTGTGGATGTGAATTATGGTGGAAGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgacttcatacaacgcacttttatattttcattattttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC
                  acttttatattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattgttttggcaaactttttatgcatgggttctcttaatgagtaatgacttcatacaacgcacttttatattttcattattttgtttgaatatttcagGTGGACCAACTGCTGAAACACGTGGAATTTTAAACTTGAGCATTCAGTACTGGACTAGTCGGGGTTGGGCATTCGTTGATGTTAATTATGGTGGAAGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - tgttttg
- - - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - gacttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg