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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggtatcttcattttaagatttgtgttattatgctgttctagtgacaggtaaaagttttgaagttatatctgactgcttgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA

Basic information

species Glycine max
transcript GLYMA06G00300.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G088737_T01 (Zea mays), 3'ss of exon 6
ggtatctt-cattttaagatttgtgttattatgctgttctagtgacaggtaaaagttttgaagttat-atctgactgct--tgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA
  ||| || ||    |   |     |  | ||||   | |  |||||  ||  | ||    | |  |  |||  |   |  |||  ||| |  |    |   |||||  |||| | ||| |||||||| |||||||||||||||||||| || ||||| || ||||| || ||| | || | |||||| ||  | |||||||||
attatgttgcagcgcactgtgaacttgctcatgca--tttgatgaca--taggaattaaacaatcgttgtcttcccattactgaagtatttacttgcctaccagGTACTCTTACACGGCTGTGGTTCTCAATTTCAGTCAGTCATGGGCCTTATACTGTCTCGTTCAGTTCTATGCTGTGATAAAGGATGAGTTAGCTCATATA

upper sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G373717_T01 (Zea mays), 3'ss of exon 5
------------------------ggtatcttcattttaagatttgtgttattatgctgttctagtgacaggtaaaagttttgaa--gttat-atctgactgct--tgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA
                        | | |   ||| |      |   || |   ||||  |  | |    || | | |   ||||   | ||   ||  |   |  ||| |||| |  |    |   |||||  |||| | ||| |||||||| |||||||||||||||||||| || ||||| || || || || || || || | |||||| ||  | |||||||||
gtaagaggcatatactttttttttgttttgcacatgtgctagctctggtcaacttgctcatgcatttgatggcataggaaatgaacaatcattgccttgccattactgaactatttacttatctaccagGTACTCTTACACGGCCGTGGTTCTCAATTTCAGTCAGTCATGGGCCTTATACTGTCTCGTCCAGTTCTACACCGTGATAAAGGATGAGTTAGCTCATATA

upper sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 5
-------ggtatcttcattttaagatttgtgttattatgctgttctag--tgacaggtaaaagtt--ttgaagttatatctgactgc--ttgagctatctgg----taca------------tttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA
       |  |   |  |   ||||   ||| ||  || | | |  |   | | |    ||| |   ||  |  |||    |||||   |  || || | |     |||             |||||||||| |||||| ||||||| ||||| ||||| |||||||||||||| || ||||| || ||||| || |||   |  || || || || || || || || 
gtacgttgagacaattttgacaagaacagtgctaacatacagattgaccttaagaaacgaaaatcagtttcatctatgatggactgtgatcaagatagcagcatcttaccattgttttcttttttgtagGTACCCTTATTTGGCAGTTGTTCTAAATTTTAGTCAGTCATGGGCATTATACTGTCTGGTTCAGTTCTATGGTGCAACGAAAGATGAGCTTGCACACATC

upper sequence: GLYMA06G00300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 6
ggtatcttcattttaagatttgtgttattatgctgttctagtgacaggtaaaagttttgaagttatatctgactgcttgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA
 |||   |  |||  | ||   ||||   |   | ||    ||  |  |  |  | || || |  | ||| || | |  ||   |||| |   |||||||||||||||| || ||||||||||| ||||||||||| ||||||||| |||||||| ||||||| |||||||| ||||||||||| ||| |||  || |||
-gtaagatagtttggaaataattgttggaaaattttt----tgctaacttgatttgtttaaat-gtctcttacagttgtagacttctgtt---tttgtagGTATCCTTACATAGCAGTGGTTCTAAATTTCAGTCAATCATGGGCTCTGTACTGCTTAGTTCAGTTTTATACTGTTACAAAGGATGAATTGGAGCACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtaaaagttttgaagttatatctgactgcttgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA
                     atctgac  putative branch site (score: 3)
         ttttgaagttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtatcttcattttaagatttgtgttattatgctgttctagtgacaggtaaaagttttgaagttatatctgactgcttgagctatctggtacatttgtagGTATCCTTATATGGCAGTGGTTCTGAATTTCAGTCAGTCATGGGCTTTGTACTGCCTAGTTCAATTTTATACAGTTACAAAGGAAGAACTGGCTCATATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - -cttcatt
- - - - - - - - - tttgtgt
- - - - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctatctg