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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatatggtactagttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC

Basic information

species Glycine max
transcript GLYMA19G24620.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 3'ss of exon 6
tatatggtactagttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttca------aaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
     | || |  |  |  | | ||||| ||    |     ||| ||| ||||   ||  |  | |      ||| | ||   ||        | |  || | |||||  | |||||  | ||||| ||||| ||||| |||||||| || || || ||||| || |||||||  ||||| ||||| ||||||||||||||||| |
-----gttatttttctagctgtaatttt-tcaagctggttgtgttctgttatttgctttctgcagtgtgcaacattagtaaactctctggttgatttgtattctagATCCGTGAGGGTTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCTATGCCCAAGATGCTTATAGATGGAGCTGTTGAATATGAAGATGGTACTC

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g70960.1 (Oryza sativa), 3'ss of exon 5
-tatatggtactagttcatatatcattttg--tccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
 |   || ||  ||| | | | | ||| |   |||   ||  |   | |  | |||   || |  |   || |  | |      |||   | |   ||| |||||  | || ||  | ||||| ||||| ||||| |||||||| || || |||||||| || ||||||| |||||| || || || ||||||||||| || |
ttgcctgctaa-agtgcttctgttattgttactcctcctagtgcactccctaaatttgcttttgcagtgtcctaaccttctggcgtt--gatttgaaatttagATTCGTGAAGGCTTGCATTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCCAAGATGCTTATTGATGGAGCAGTCGAGTATGAAGATGGCACTC

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G158479_T04 (Zea mays), 3'ss of exon 5
---tatatggtactagttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
   ||    |  |   ||  | |  | | | | |  |  | | |||  ||  | || |  || ||| |      | |  ||| || |  |  |   |   |||||  | ||||| || || || ||||| ||||| |||||||| || || |||||||| || |||||||||||||| ||||| || ||||| |||||||| |
gcataccaaggtcaccttggtttgccttgtcgcctttgaaaccatg-gctcttgttat-ctcgtaatcaaaccataaaaactttggtttatttg-catcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCCATGCCGAAGATGCTTAATGATGGAGCTGTTGAGTATGAGGATGGTACAC

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 3'ss of exon 4
tatatggtactagttcatatatcattttgtccctatacc-gatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
           | ||  | |   |||||  |  || ||  | | |    |  |    || ||  |  | |    || |   |||    ||      |  |||| |||||||| || || || |||||||| || |||||||||||||| || ||||| |||||||| || ||||  |||||||||||||||||||| || |
--------gtaaatttctctcctatttttgctttagacttgttattacaacttcaaattgttggaagt-tagaaataatcctgtgactaacg--ggtacagATCAGAGAGGGGCTACACTACAATCCTTATTTCCCTGGTGGAGCAATCGCTATGCCAAAAATGCTCAACGATGAAGCTGTGGAATATGAAGATGGAACTC

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 3'ss of exon 5
tatatggtactagttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
                     | | ||| || |  |  | |  |     |  |  |   | ||| | ||  | ||||  |     |  ||||   |  |||| ||||||||  | || || |||||||| || ||||| ||||||||||| ||||| |||||||| |||||||  ||||| || ||||||||||||  ||
--------------------gtaagtttctctcattttccacattgaacttcttcgaattcaaagtgctggttatgaaaaatccgatgataactgtacagATTAGAGAGGGGTTACACTACAATCCTTATTTCCCTGGGGGAGCAATTGCTATGCCGAAAATGCTCAATGATGAAGCTGTTGAGTATGAAGATGGTGTCC

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv09s0002g05950.t01 (Vitis vinifera), 3'ss of exon 4
tatatggtactagttcatatatca-ttttgtccctat---accgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
     | || |  |    |  |   |||||||   ||   |  | | |      ||| | ||  | ||  |    || ||| | |  |  || |  |  |||||||  |||| || || || ||||||||||| || |||||||| ||||| || ||||| |||||||| |  ||||||||||| || ||||||||||||||||
---ccgataatcatcttgacttgggttttgtcatcatttgattgctctttctgcattcttttaatgaatgttccatcctga-tgtcattgaactctttctgtagATTCGAGACGGGCTGCACTATAATCCTTATTTCCCTGGTGGGGCAATAGCTATGCCCAAAATGCTCATCGATGGTGCTGTTGAGTATGAAGATGGTACCC

upper sequence: GLYMA19G24620.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 3'ss of exon 5
tatatggtactagttcatatatcat-tttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttca-aaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
|   || |  |  || || | | || ||| |    |||      |  ||||    | ||| |  || |  |   || |   |||||| ||||| |  |||||||  |||| ||  | || || ||||||||||| ||||| || |||||||| |||||||||||||| | |||||||||  | || |||||||||||||| |
tgc-tgatttttttttattttttatgtttatggacatattctgttcatgatgacctattcctctacctaatca-atcaagttgttcacaaatatttttgtagATCCGAGAAGGGTTGCACTACAATCCTTACTTCCCTGGGGGTGCAATTGCTATGCCTAAAATGCTCATTGATGGTGCACTTGAGTATGAAGATGGTACGC

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|193589866|gb|FK545230.1|FK545230
EST:     ATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCG                         ATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
genomic: ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCAgtaagttctt ... aataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
EST: gi|298178076|gb|HO027459.1|HO027459
EST:     ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCA                         ATAAGAGAGGGACTTCATTATAATCCTTGCTTTCCTGGTGGAGCAATTGCC
genomic: ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCAgtaagttctt ... aataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
EST: gi|208300265|gb|GE098924.1|GE098924
EST:     CGTGACCCACCTGCTGGTGTTTCG                         ATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
genomic: CGTGACCCACCTGCTGGTGTTTCAgtaagttctt ... aataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
EST: gi|151405823|gb|EV275638.1|EV275638
EST:     ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCA                         ATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
genomic: ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCAgtaagttctt ... aataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
EST: gi|13240163|gb|BG359472.1|BG359472
EST:     ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCA                         ATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
genomic: ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCAgtaagttctt ... aataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
EST: gi|254330991|gb|GR842256.1|GR842256
EST:     ATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCG                         ATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC
genomic: ATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCAgtaagttctt ... aataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC
 tactgat  putative branch site (score: 2)
                                 tatgttcaaaataata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatatggtactagttcatatatcattttgtccctataccgatgtactgatattgtgttcttaaacttcttttcatgactatgttcaaaataataatgtagATAAGAGAGGGACTTCATTATAATCCTTACTTTCCTGGTGGAGCAATTGCCATGCCTAAAATGCTTAATGATGGTGCTGTGGAATATGAAGATGGTACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - -tgtccct
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc