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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTGGAGAAAGGTGCTGTTATGAAAGCTATCTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctgactttcttttggttgtggggggatctatttttgtttacttgttagttttgaacctgaattgttttttgggttgcaaatcttctcttggcag

Basic information

species Glycine max
transcript GLYMA20G27000.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G328265_T01 (Zea mays), 5'ss of exon 6
GAAAATTGGAGAAAGGTGCTGTTATGAAAGCTATCTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctgactttcttttggttgtggggggatctatttttgtttacttgttagttttgaacc-tgaattgttttttgggttgcaaatcttctcttggcag
| ||  | ||||     |||||  | |||||||| |||||||||||||| |||||||||||||||  ||||||  ||||  |||||||   |  |    || ||           |  |  |      | | || |||  |     |    |||||||     | ||| ||||             
GGAAGCTTGAGAGGAAAGCTGTCCTCAAAGCTATTTGTGCTGGTTTTGAGGAAACTACTGAACCAAATGTTTGCCTGAGTGGTGgtaagcacatataaactatttaacacctaatgcacagtaagcagtaatttattatatggaggctacaaattgttgagctgtttgaaaatag-----------

upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 5
lower sequence: AC211785.2_FGT003 (Zea mays), 5'ss of exon 3
GAAAATTGGAGAAAGGTGCTGTTATGAAAGCTATCTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctgactttcttttggttgtggggggatctatttttgtttacttgttagttttgaacc-tgaattgttttttgggttgcaaatcttctcttggcag
| ||  | ||||     |||||  | |||||||| |||||||||||||| |||||||||||||||  ||||||  ||||   ||||||   |  |    || ||           |  | ||      | | || |||  |     |    |||||||     | ||| |||              
GGAAGCTTGAGAGGAAAGCTGTCCTCAAAGCTATTTGTGCTGGTTTTGAGGAAACTACTGAACCAAATGTTTGCCTGAGTGATGgtaagcacatataaactatttaacacctaatgcacaataagcaataatttattatatggaggctacaaattgttgagctgtttgaaaacag-----------

upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G303631_T01 (Zea mays), 5'ss of exon 5
GAAAATTGGAGAAAGGTGCTGTTATGAAAGCTATCTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctgactttcttttggttgtggggggatctatttttgtttacttgttagttttgaacc-tgaattgttttttgggttgcaaatcttctcttggcag
| ||  | ||||     |||||  | |||||||| |||||||||||||| |||||||| ||||||  ||||||  ||||   ||||||   |  |    || ||             ||  |  |   | | || |||  |     |    |||||||     | ||| |||              
GGAAGCTTGAGAGGAAAGCTGTCCTCAAAGCTATTTGTGCTGGTTTTGAGGAAACTACAGAACCAAATGTTTGCCTGAGTGATGgtaagcacatataaactatttaacacctaatattcagtaatcagtaatttattatatggaggctacaaattgttgagctgtttgaaaacag-----------

upper sequence: GLYMA20G27000.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 5'ss of exon 5
GAAAATTGGAGAAAGGTGCTGTTATGAAAGCTATCTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctgactttcttttggttgtgggg------------ggatctatt------tttgtttacttgttagttttgaacctgaattgttttttgggttgcaaatcttctcttggcag
|||| |||||||||||||||||| |||| || || ||| |||||||||| ||||| ||||| |||| ||||||||||||  |||||||    | ||  |   || | |     |              |||| ||       | | || ||  | ||||||    || |  | ||||||   | |  | |||| || ||||||
GAAAGTTGGAGAAAGGTGCTGTTCTGAAGGCCATTTGTTCTGGTTTTGAGGAAACCACTGAGCCAGATGTTTGTTTGAGTGGTGgtaagcttttaccataagttagatactaagttcggtatatccaaatctcttgattgactcgcttgctcatcagttttccttctaatctatttttttaatgg--attcttttcctggcag

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|7233271|gb|AW568619.1|AW568619
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|208216537|gb|GE012525.1|GE012525
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGA
EST: gi|16997296|gb|BM086668.1|BM086668
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|193445332|gb|FK409385.1|FK409385
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|37994040|gb|CF805786.1|CF805786
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|193348579|gb|FK317711.1|FK317711
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|193626746|gb|FK573670.1|FK573670
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|151400595|gb|EV270409.1|EV270409
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCGGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|208326073|gb|GE119727.1|GE119727
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|151407733|gb|EV277548.1|EV277548
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|298171587|gb|HO021179.1|HO021179
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|15286008|gb|BI469899.1|BI469899
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|192304755|gb|FG994991.1|FG994991
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
EST: gi|193667036|gb|FK608882.1|FK608882
EST:     CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAAT
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAAT
EST: gi|193696330|gb|FK640178.1|FK640178
EST:     CTGTGCTGGTTTTGAAGAAACTACCGAACCAGCTGTTTGTTTGAGCAGTG                         ATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA
genomic: CTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctg ... ctcttggcagATGTGGAGACAAATGAGTGTTTGGAGAATAATGGTGGTTGTTGGCAGGATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAATTGGAGAAAGGTGCTGTTATGAAAGCTATCTGTGCTGGTTTTGAAGAAACTACTGAACCAGCTGTTTGTTTGAGCAGTGgtaaatgctgactttcttttggttgtggggggatctatttttgtttacttgttagttttgaacctgaattgttttttgggttgcaaatcttctcttggcag

- - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG