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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctctgcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA

Basic information

species Glycine max
transcript GLYMA02G25290.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g08840.2 (Oryza sativa), 3'ss of exon 3
accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctctgcact--ctcctgactttaat-gtcatcgactttttt--ttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA
|       ||   ||| | |  |  | |  |    | |  ||    |  | |  |||| | | ||  ||| |||  ||||  ||  | |  | |  |  | ||||| || ||||| ||||||||||| ||  | |||||||| ||||| || ||||| || || | |||||||||||| || ||||| ||||| |||||||||||
attgtttcca---gtggtctggt--cttgctcaggttagctcaggcaggtcttctcctgttctctttctcttgatgttaacagttgttgtttctcctcataccagGATTCATGGGTGCCATGATATCAAACCTTGCATTTGTTTTCCGCAACATCTTCTCAAAGAGGGGCATGAAGGGGAAATCTGTCAGTGGCATGAATTACTA

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G180720_T02 (Zea mays), 3'ss of exon 3
---accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctctgcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA
   || ||    |||  | |  ||     | |||   |    |   | |  ||  | |  | | ||     || |  ||  |  | |   |  ||    ||||| |||||||| ||||||||||| ||  | |||||||| ||||| || ||||| ||||| | |||||||||||| ||||| || ||||| |||||||||||
tagactaaatttaagcttaagatagagataaaatacgagtcatggacttgttttcaattgtttccaaaggtctaatgtt--ttccgtttgcccttcca-ccagGATTTATGGGTGCCATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTCCGTCAGTGGCATGAATTACTA

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G431314_T01 (Zea mays), 3'ss of exon 3
--accaagcgcaagtgtgatttacttgcataa-tggtatcatttctcataattatagtcctctgcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA
  |  |     |||  | |  ||     | || | | |    |   |||| ||  | |  | | ||   |      ||||    |||   |  |    |||||| |||||||| || |||||||| ||  | |||||||| ||||| || ||||| ||||| | |||||||||||| ||||  || ||||| |||||||||||
agaatagatttaagcttaagatagagaaaaaaataggagtcatagacatatttgcaattgtttccaaggtataatgttta---ccatttgccctcccctccagGATTTATGGGTGCTATGATATCCAACCTTGCATTTGTTTTCCGCAACATCTTCTCGAAGAGGGGCATGAAGGGGAAGTTCGTCAGTGGCATGAATTACTA

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 2
---ac-caagcgcaagtgtgatttact---tgcataatggtatcattt---ctcataattatagtc-ctctgcactctc----ctgactttaatgtcatcgactttt-ttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA
   ||  |        | | ||||  |   | |||   ||| | |||     | | | ||  | |  || ||||   |      || ||| ||       |    ||  ||| ||||||| ||||| || ||||| ||||| ||||| || || |||||||| ||||| ||||| ||||| ||||||||||||||||| || || ||||| |||||
gtaacatatatcttcatcttatttgttagatacattgaggtgtaattgggattgagatttgaaatggctttgcatgtttgattttggcttcaaatctgctgctccttacttttcagGTTTCATGGGAGCTATGATTTCGAACTTGGCTTTCGTGTTCCGTAACATCTTCTCGAAGAAGGGAATGAAGGGAAAGTCTGTGAGCGGGATGAACTACTA

upper sequence: GLYMA02G25290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0177g00300.t01 (Vitis vinifera), 3'ss of exon 2
accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctct--gcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA
|      ||||  |  ||||    |      || ||    | | |    |||  |||| |  |  ||  |||||  ||   ||    |  | | | |  ||||||||||||| |||||||| |||||  |||| ||||| || || || || ||||| || |  ||||||||||| |||||||||||||||||||| |||||
attttttgcaaaagacattttgggggggttaggaatgtaattttactcctattttccttttagggctgacctgaacttg--gtaggtgcttgtctgtatcagGTTTTATGGGAGCCATGATTTCGAACCTGGCTTTTGTTTTTCGCAACATATTTTCAAAGAGAGGCATGAAGGGGAAGTCTGTTAGTGGAATGAACTACTA

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|26058858|gb|CA801772.1|CA801772
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|5770929|gb|AI974103.1|AI974103
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|21285521|gb|BQ473392.1|BQ473392
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|5770799|gb|AI973973.1|AI973973
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|254314323|gb|GR824564.1|GR824564
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|298199165|gb|HO042528.1|HO042528
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATAATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|18734052|gb|BM527958.1|BM527958
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|17518575|gb|BM187617.1|BM187617
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
EST: gi|298191223|gb|HO038702.1|HO038702
EST:     TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCG                         GTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT
genomic: TGGTGGATGTGCACTTGCTGCTGTGACTGAGCTCAATTTCAATATGATCGgtagggaact ... ttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattatagtcctctgcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA
                                      tcgacttttttttcc  CT-rich tract
                                         actttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
accaagcgcaagtgtgatttacttgcataatggtatcatttctcataattatagtcctctgcactctcctgactttaatgtcatcgacttttttttccagGTTTTATGGGGGCCATGATATCGAATTTGGCATTTGTATTCCGTAATATCTTTTCGAAAAAGGGCATGAAGGGAAAGTCTGTTAGTGGAATGAATTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
-ccaagcg
- - - - -aagtgtg
- - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtcatc