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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

Basic information

species Glycine max
transcript GLYMA02G39360.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 24
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
        || || | ||   |||||  ||   |  || |   |   | |||       |||   |   | ||||  |  |        || || |  |||| ||||||||||| || || ||||| |  ||||||||||||||||| || |||||||| || || || ||||| ||||| || |||||||||||||| |
------gtatatata-caggagcaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacacccttttttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 24
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
    | | || || |  |    |         |  | | | | || | ||      | || |    |   |  || ||||  | |||| || || |  |||| ||||||||||| || || ||||| |  ||||||||||||||||| || |||||||| || || || ||||| ||||| || |||||||||||||| |
----gtatatatacaggaccaacctgttagaactaaaacatatttcagtacaagtcttttcttatctagattttttctaacaccctttttt-ttgtatagGTTGATGATTTGGAGGAAGTAAGTGAATACTACCAGAACAGAGGATGTTTCAATGAACTTATTTCCCTCATGGAAAGTGGTCTAGGACTGGAGCGTGCTC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
----attgggaaatgtagaacattggcaaca------agtggcagatagacagttga--ttagtttgttattttctgttgtttgattactaattctcttt---attattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
    |   | |   | | |   |||  ||        |||  | | |  | ||  ||  ||   |   | |  ||| || |||  |  |  ||   ||||   ||| || |  |||| ||||| |||||||| || |||||||  ||||| || ||||||||||| |||||||| ||  |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
----attgggaaatgtagaacattggcaacaagtggcagatagacagttgatt---agtttgttattttctgttgtttgattac-taattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
    |   | |   |   |   |||   |    |  |   |      || |||   |  ||  |||  | | ||  ||  | || ||  |    || || || |  |||| || ||  ||||||| || |||||||  |||||||||||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
----attgggaaatgtagaacattggcaacaagtggcagatagacagttgattag---tttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
    |   | |   | | |   |||  ||    |   ||   |     | |       | | | || |  |  ||| |||    |     | | |||| || |  |||| ||||| |||||||| || |||||||  |||||||| ||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagcacatacttgataattttttctagtctgttttataacagagcttctatgatctatttctgtctgacatgtctgattttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
--------attgggaaatgta---gaacattggcaacaagtggcagatagacagttga--ttagtttgttattttctgttgtttgattactaattctctt-tattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
         | ||   |  ||    |  |||       |||  | | |  | ||  ||  ||   |   |||  ||| || |||  | |    | || || |||| || |  |||| ||||| |||||||| || |||||||  ||||| || ||||||||||| |||||||| ||  |||| ||||||||||| |||||||| || ||||| |
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------attgggaaat-gtagaacattggcaacaagtggcagatagacagttgatt---agtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
                                                                        ||    || | | ||  |||     |    |  |   |      || |||   |  ||  |||  | | ||  ||  | ||  |    || | || || |  |||| |||||  | ||||| || |||||||  |||||||||||||||||||| | |||||| ||  |||| ||||||||||| |||||||| || ||||| |
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 24
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctg----ttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
| ||      |     ||||   |||    |   | ||  |  || |  |   |  |  | | ||     | ||||||     ||  |  |||| ||| |  ||||||||||||||||||| || ||||| | |||||||||||| |||||||||||||| || |||||||| |||||||||||| | ||| |||| ||||| |
aatgcagctagctattcatttataacctcagtatgttactctatttagaatcctagtcctgtttgaatcctctttgatcttggatatt--ttatgattct--agGTGGATGATTTGGAAGAAGTCAGTGACTATTACCAGAACAGGGGATGCTTTAATGAGCTCATATCTCTCATGGAGAGTGGATTGGGATTGGAACGTGCAC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattac-taat----tctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
    |||    | ||   |  |   ||||| |   ||  |  | |  ||  ||| |      ||        ||||  |||     ||    |    || || ||||||| |||||||||||||| ||||| | ||||||||| |||||  ||||| |||| || || || || ||||| ||||| |||||  ||||||| || |
----ggagtattggattctctggtccaagtagagtatgcattgatt-ttgttttctggaaggctagaaaacaattatataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTC

upper sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 24
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 24
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
                                  |  || |  | | ||   | |||||  ||| |  |||| ||  |        ||||||  ||  |||||||||||||||| || || ||||| |  |||||||| || ||| | ||  |||||||||| ||||||||||| ||||| |||||||| || || || |
----------------------------------gtaaggctatagttt--ctggttatactctatc-tttggttggtctaatctgttattaa-atccagGTGGATGATTTGGAGGAAGTGAGTGACTACTACCAGAATAGGGGACGATTCGATGAACTGATTTCTCTAATGGAAAGTGGTCTTGGACTCGACCGCGCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC
                             tactaat  putative branch site (score: 1)
                                   ttctctttattatt  CT-rich tract
                       tttgattactaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgggaaatgtagaacattggcaacaagtggcagatagacagttgattagtttgttattttctgttgtttgattactaattctctttattattatgaagGTGGATGATTTGGAAGAGGTTAGTGAGTTTTACCAGAACAGAGGATGCTTTAATGAACTGATATCTCTAATGGAGAGTGGACTTGGACTGGAGCGTGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - -aatgtag
- - - - - - - - - - - - -caagtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctgttg