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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG

Basic information

species Glycine max
transcript GLYMA07G00330.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaat-gcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                    ||   || | |||||   | | |   ||||        ||      |  ||| |    |  | |||| | || || || |||       ||||| || ||||||||||| ||||||||  |||||||||| || |||  |||||||||||||||||| ||| ||||| ||||  |||||||| | |||||||
-----------------------------------gtaaattt-tcagtaatggataatgactatt--------cagacaatatgtcacttctgtggggtactgagatcgcttaaattgaa----cagGTATTGTGTATGCTTGCATGTTGGGTTAAAGATCCAAATGGGGATTATTTCAAGAAGCATCTTGCTAGGATCCCATATTATATATGGGTTACAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                            | | |    |  | |   || | ||  ||   | ||   ||   |||   |  | | |||| |||  |  | ||   |   |||| || ||||||||| | |||||||| |||||||||||||| |||  |||||||||||| ||||| ||| | ||||||||  ||||||||   |||||||
-------------------------------------------gtaatttttctgcaatggataatgtctattcagacagtatatctcttctt-tggggtgctaatatggcttaaattgaat---agGTGTTGTGTATGCTTTCATGTTGGGTTGAAGATCCAAACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 3'ss of exon 3
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                              |  |  ||   |  | |  |    | || || ||| ||   |   || | | ||   | ||||  | | |   ||   ||||| || |||||||||||||||||||| ||||||||| | || ||| ||||||||||||| ||||| ||| |||| |||||  ||||| |  | |||||||
--------------------------------------------gtaacacgattgtccgtgttatgagatgtttaaaaggaaa---aagaaactctaatcgaagaatgtctct-taaattgagcagGTATTGTGTATGCTTGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTCCCGGATTATATATGGATGGCAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                      |  || |  | |    | |  || |||||        |      |  ||| |    || |||||| | |||      |   ||   ||||  || ||||||||  | |||||||| ||||||||||| || |||  |||||||||||| ||||| ||| |||||||||   |||||||| | |||||||
-------------------------------------gtttttttctgcagtggataacttctattt--------agacaatatgtcagttctttaggatactgatatg---gcttaagttgaacagGCATTGTGTATGCTCACATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTTTATATGGGTTGCAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 5
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                    |||  || | |||||   | | |   ||||        ||| | |  | || ||    |  | |||| | || | |  | ||      ||||| || ||||||||  | |||||||| ||||||||||| || |||  |||||||||||| ||||| ||| ||||||||||  |||||||| | |||||||
-----------------------------------gtattttt-tcagtaatggataatgactattcaga----caatatgtcactccttt---tggggtactgatatcccttaaattga---acagGTATTGTGTATGCTCTCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                   | ||  || ||      ||||          |  || ||||    | |  ||| |    |  | | |||| |||      |   ||   |||||  | ||||||||| | |||||||| ||||||||||||||  ||  |||||||||||| ||||| ||| | ||||||||  ||||||||   |||||||
----------------------------------gtaatttttctgcaatggataa----------tgtctgttcagacagtatatcacttctttggggtgctaatatg---gcttaaattgaacagGTACTGTGTATGCTTTCATGTTGGGTTGAAGATCCAAACGGGAATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaat-gcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                    |||  || | |||||   | | |   ||||        ||      |  ||| |    |  | |||| | || || || |||       ||||| || |||||||| || |||||||| ||||||||||| || |||  |||||||||||| ||||| ||| ||||||||||  |||||||| | |||||||
-----------------------------------gtattttt-tcagtaatggataatgactatt--------cagacaatatgtcacttctttggggtactgatatcgcttaaattgaa----cagGTATTGTGTATGCTCGCATGTTGGGTTGAAGATCCAAATGGGGATTATTTCAAGAAGCACCTTGCTAGGATCCCAGATTATATATGGGTTGCAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 11
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                             | |||||| | |  |||  |||  |               || ||||    | |  ||| |    |  | | |||| |||      |   ||   ||||| || ||||||||| | |||||||| ||||||||| |||| |||  |||||||||||| ||||| ||| | ||||||||  ||||||||   |||||||
----------------------------gtattttttctgca-atggataatgt---------------ctgttcagacagtatatcacttctttggggtgctaatatg---gcttaaattgaacagGTATTGTGTATGCTTTCATGTTGGGTTGAAGATCCAGACGGGGATTATTTCAAGAAGCACCTTGCTAGGATTCCAGATTATATATGGGTTGGAGAAGATG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv09s0054g01210.t01 (Vitis vinifera), 3'ss of exon 7
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttc--cagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                                                     |||       ||| ||| | | | ||         || |||    |  ||||    |   |  ||   ||   ||||| || |||||| ||||||||||||| ||||||||| | || ||| ||||||||||||| ||||| ||| | ||||||||  ||||| || | |||||||
----------------------------------------------------gtaa---cacgattgtccgtattatgaaa-----tgtttaaaagaaactctaacgaactctttcttcaattgagcagGTATTGTGTATGTTTGCTTGTTGGGTAGAAGATCCATATGGGGATTCTTTCAAGAAGCACCTTGCTAGGCTGCCAGATTATATATGGATTGCAGAAGATG

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|8669059|gb|BE190161.1|BE190161
EST:     ATTATGAAGATGAGACTAGTCGATACATAACCATTGGTTGTGTGGAAAAG                         GTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTC
genomic: ATTATGAAGATGAGACTAGTCGATACATAACCATTGGTTGTGTGGAAAAGgtaggtgtca ... ttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTC
EST: gi|4301834|gb|AI443247.1|AI443247
EST:     ATTATGAAGATGAGACTAGTCGATACATAACCATTGGTTGTGTGGAAAAG                         GTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTC
genomic: ATTATGAAGATGAGACTAGTCGATACATAACCATTGGTTGTGTGGAAAAGgtaggtgtca ... ttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG
                           tactaaa  putative branch site (score: 1)
                                       tatattttttttcc  putative PPT
               attcaaatatgatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtgtcataacaataatgcatattgattttttttatccttatgagtaaaataaactttttattttccttttcaagagggaattcattcaaatatgatactaaaatgcatatattttttttccagGTTTTATGTATGCTTGCTTGTTGGGTGGAAGATCCAAACGGAGATGCTTTCAAGAAGCATCTTGCAAGGGTCCCAGATTACTTATGGGTTTCTGAAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG