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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcataaatacctataagaacaagaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG

Basic information

species Glycine max
transcript GLYMA06G11120.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 7
tgcataaatacctataag--aacaagaaactttgtgccaatcttat-tttggtatgatttgtttggcaaagtttagaaactaataggcatatggatttttt--agGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
 |  |      ||   ||  | ||||| | | | ||     |   | ||| ||     | |||       || |    |  |  ||  |      ||| ||  |||||||||||||||||||||| ||| |||| || |||||||||||||| ||||| || ||||| || |||||||| |||| | | ||  | |||
-gtttgttcttcttgtagttatcaagagattgtttggattgcaagtgtttagtgcccatagttaactctggtctttctaacatgagtaactcaactttcttgcagGTTCATAATGATGATGAGGTTAGGACATTATTTAAGCAAGTTCAAGGCGAAGTACCTGGTTCCCCAATATTTATCATGAGGCTAGCTGCTCAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 3'ss of exon 3
-------------tgcataaatacctataagaacaagaaactttgtgccaat--cttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
             |   | || || ||| ||||  | || |    |  |||   |  ||   |  |||| |        |  |||| ||   ||     | ||  |  ||| ||||| ||||||||||||||||| || ||| |||| ||||||||||| || ||||| || || ||||| |||||||| |||||||| ||||| |||
gttggttttcttttagttcaacac-tatcagaatgataagcaa-atatcaactgcacataaagaaatgaataacggaagatggttttgatgttat----cttaatggatttgtagGTACATAATGATGATGAGGTGAGAGCACTGTTTAAGCAAGTTCAGGGAGAAGTCCCTGGCTCACCTATATTTATTATGAAGGTGGCATCTCAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G377341_T02 (Zea mays), 3'ss of exon 3
---------------------------------tgcataaatacctataagaacaagaaacttt--gtgccaatcttattttggtatgatttgtttggcaaagtttagaaact--aataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
                                  |         |||| | || |   || ||   ||  ||  |  |   | | || |  |||     |   ||  |  | |   ||      |||||| | | |||||||||| ||||||||||| |||||  ||||||||||||||||||| ||||| || || ||||| |||||||| ||||| || ||||| |||
gtttgttttctttttcaactgaactgtggaaagagagggggccgctattaaaaaagtgaagttaaagtttcaggcaaaaaatag-atcaactgtcactaatttttctgtcatttgcatcattgcatggatctgt-agGTTCATAACGATGATGAGGTGAGGGCGCTGTTCAAGCAAGTTCAAGGAGAAGTCCCTGGCTCACCTATATTTATTATGAAAGTGGCATCTCAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 5
tgcataaatacctataagaacaagaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
    | ||   || |  ||||     || || ||  | | |  | | || |    |   ||  |    || | |   | | |  || ||     |  ||||||||||||||||||||||| || ||  |||| |||||||| ||||||||||| || || || || |||||||| |||| | |||||||||||
---gtgaac-tctctgtgaactgtgcacattatgg-agtttggtgtgggga--gctaactttccctttttgatatgattaaaatca-attcccctggtagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTATCATGAGGCTTGCATCCCAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 5
---tgcataaatacctataagaacaa-----gaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
   ||| | | ||  |     ||| |     |||    |||||  ||   | |||||| ||    | |   |    ||| || |  | ||      |     |   |||||||||||||||||||||| || ||  |||| |||||||| ||||||||||| || || || || |||||| | |||| | |||||||||||
gtgtgctttattatgtgattaaactatctgtgaagaactgtgcacattggagtttggtgtggggagct-accccccttttgacatgattaaatcattttccctggcagGTTCATAATGATGATGAGGTTAGAGCGCTGTTTAAGCAAGTACAAGGTGAAGTCCCTGGCTCCCCAATATTTGTCATGAGGCTTGCATCCCAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 4
tgcataaatacctataagaacaagaaactttgtgccaatcttattttggtatgatttgtttggc-aaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
                       |     || ||   || | | | |    |  |    |  || ||||| ||   | |  |||   |     ||  | |||||||||||||||||||||| |||||  | |||||||||||||||||||| || ||||| || || |||||||||||||||||||| || |||
-----------------------gtctgcttctgtagatatgactgtcactttttccactaagccaaagtgtacttattg-tagtttttcattttggtaagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAAGGTGAGGTCCCGGGCTCGCCGATATTTATAATGAAGGTTGCTTCACAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 4
tgcataaatacctataagaacaagaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
              | ||     | |  | ||   |  | | ||| |||  | |   | ||   | |   ||   ||| ||     | |  | ||| ||||||||||||||||||||||| |||||  | |||||||||||||| ||||| || || || ||||| ||||| |||||||||||||| || |||
-------------gtcagcttctgtagatatg---ccttttgattgtggactaagccgattactata---taagtacttattctggttttaaatttatagGTTCATAATGATGATGAGGTTAGGGCTCTATTCAAGCAAGTTCAGGGTGAGGTCCCAGGCTCACCAATATTCATAATGAAGGTTGCGTCACAG

upper sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 4
tgcataaatacctataagaacaagaa-actttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatg-gattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
    | |     |||    | | ||  | ||||  |     | |||||  ||  |||| |      || |  ||  |    ||  ||| |  ||  ||||||||||||||||||||||| || | ||| ||||||||||||||||||||||||||||| || || |||||||| |  ||||||||||| ||||||
gaagtcacgggttatgttgagatgattagtttggactgtcatgattttccta--atttctcaactgaaatgaagttaaccttattcatttttgaacttttagGTTCATAATGATGATGAAGTCAAGGCTTTGTTCAAGCAAGTTCAAGGTGAAGTTCCTGGCTCCCCCATATTCACGATGAAGGTTGCTTCCCAG

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|192305788|gb|FG995730.1|FG995730
EST:     CTGCAATGATCAAGGCATCTTGGAGTGGTGGTGGTAAAGGAATAAGAAAG                         GTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAA
genomic: CTGCAATGATCAAGGCATCTTGGGGTGGTGGTGGTAAAGGAATAAGAAAGgtttgcttct ... gattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG
                             aactaat  putative branch site (score: 2)
                                               tttttt  putative PPT
                       tttagaaactaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcataaatacctataagaacaagaaactttgtgccaatcttattttggtatgatttgtttggcaaagtttagaaactaataggcatatggattttttagGTTCATAATGATGATGAGGTAAGGGCATTGTTCAAGCAAGTTCAAGGTGAAGTTCCGGGTTCACCCATATTTATAATGAAGGTTGCATCCCAG

tgcataa
- - - - - - - -aagaacaa
- - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - -ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatatg