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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT

Basic information

species Glycine max
transcript GLYMA19G22590.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
--atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
    |   || | || |    ||||  |    |  |    |    |         || | |    ||  |  |  |||    |  |||      || | |||||| || ||  |  |  | || ||||| |||||||||||||| || ||||| || ||||| ||||| |||||||| || ||||| || || || ||||| 
gtcagtcctactatctt----cttcatcttcatctgaacgaagaacacacgaacgaaccaagaaattaatctaactgaattcttgaat------ttttgcagGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC

upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G127338_T02 (Zea mays), 3'ss of exon 1
atg-gtataatgtcatgaaacttcggcacggttagtgtaacttgctttt----tttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
 || |||   |  | ||  |  |  |  |   | || | |||  || |        ||||| ||  ||| |  |    ||       | |||    | ||| |||||| || ||  |  |  | ||  | || || ||||||||||| |||||||| || ||||| ||||| |||||||| || ||||| || || || || || 
gtgcgtacgctagcttgctagctgtgtgcctgt-gtctgactgactctgagcgcgcttaaattagatgtatcatatcatg-------ccatgcatgcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCGGGCAAGCGCTTC

upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G40780.2 (Arabidopsis thaliana), 3'ss of exon 2
atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
   ||| |||  |   ||||     | |||||  | | || |        ||||    || | ||    | ||| |  |||    |||  |||| | |||||| || ||  |  |  |  |  |  | |||||| |||| || || |||||| ||||||||||||| || ||||||||||||||||| ||||| || |||
---gta-aattcccctaaaccaaaac-cggtttattttacctaaaccggattta--tcaaatcttaaccggtttta--att----tgttttctttt-cagGGGACCGGGAATTGCAGTGTTGGTTTTGTCATGGGTCATAACACTATACACATTATGGCAAATGGTGGAAATGCATGAAATGGTTCCTGGAAAGCGTTTT

upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G48640.1 (Arabidopsis thaliana), 3'ss of exon 2
atggtataatgt-catgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgaga-attacaatgtcctcttataca-----gGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
    |  |||    ||| |  ||    |    |    ||  |   |||  |||| |  | | |  |  |  ||| | || ||||||| ||| | ||||| |     |||| |||||  || |  | || || || |||||||| || || || |||||  ||||||||||||| ||||||||||| |||||||| |||||||| |||
----ttgaatacatatgtagttttttaatttcttac-tacataaatttacttttgatttgattagtaat--attcgtgatattacaaagtcttgttatatatgttagGGGACCAGGCATAGCAGTCCTGATACTATCATGGATAATAACACTTTACACGTTATGGCAAATGGTGGAGATGCATGAGATGGTTCCCGGAAAACGCTTT

upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0171g00400.t01 (Vitis vinifera), 3'ss of exon 2
atggtataatgtcatgaaacttcggcacggttagtgtaacttgcttttttt-ttaaactaagtgtttgttgatttgagaattacaa---tgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
   ||||  | |  ||   |||    |  | |||| |  |||  | ||| | |   | |   | |   |    ||||  || | ||   | |     | | ||||||||| |||||    ||| |  | || ||||||||||| || || ||||||||||||||||||||||||||||| || |||||||| || ||| |||||
---gtatg-tcttttgtgtctttacaagagatagt-tgccttattatttatgtctgattccatttgattaaggttgaacataaaaaaaatattgatcttttcagGGGTCCTGGTGTGGTGATAATGGTGCTATCATGGATCATTACTCTTTACACACTATGGCAAATGGTTGAGATGCACGAGATGGTTCCTGGGAAAAGGTTT

upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S79_71V6.1 (Physcomitrella patens), 3'ss of exon 3
atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgtt---------gatttgagaattacaatgtcctcttat--acagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
   |||| |   ||  | ||  | ||  | | |   |  ||| || ||||  |      | ||||   |           |||||| || ||   |   || | |    |||||||||||| |    || || ||||| |||||| |||||||||| | |||||| ||||||||||| |||||||| |||   || || ||||| || || 
---gtatca-accactacaccacagccagttcacgtttccttcctattttccttccgccattgttcccttctccacaaactttgaggatgacgtgggtatcatgtttgtagGGGTCCAGGTCTCCTAATGCTCATCCTTTCATGGGTCATCACCCTCTTCACACTCTGGCAAATGGTGGAGATGCACGAAGCTGTGCCCGGAAAGCGATTC

upper sequence: GLYMA19G22590.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
                                   ||||| | |   | || |||       || |     ||| ||  ||      | |  || | |||||| || ||  |     | ||  ||||||| |||| | |||| || ||||| |||||||||||||| |||||||| || |||||    || || || || 
-----------------------------------gtaacgttcgaatgttataa------cgtctacattttttagggttc-----ttcgtttttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTC

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|254342919|gb|GR859081.1|GR859081
EST:     CCCTATGCCATGTCAGAGCTTGGATG                         GGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACAC
genomic: CCCTATGCCATGTCAGAGCTTGGATGgtatatttca ... tcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT
                    tgttgat  putative branch site (score: 4)
                                        tgtcctctt  putative PPT
     tttaaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtataatgtcatgaaacttcggcacggttagtgtaacttgctttttttttaaactaagtgtttgttgatttgagaattacaatgtcctcttatacagGGGTCCAGGTGTAACTATACTTATCCTCTCATGGATCATCACCCTGTACACACTATGGCAAATGGTTGAGATGCATGAAATGGTTCCAGGAAAACGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - catgaaa
- - - - - - - - - -cttcggc
- - - - - - - - - - - - - - -gttagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgtc