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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

Basic information

species Glycine max
transcript GLYMA10G35230.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 6
gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatg-ctttactgtttcca---tgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
   ||   |   | ||| |   ||||||  || | | |  || |  || |  | |  |  |  | || |  ||  ||   ||   ||||||| |     || |||||||||||||||  |||| ||||||| |||||||| ||||||||||| |||||||||||  || | ||||||
---gtcagatcttgtgtga---agttgtagtaaacatagtatcacaatatgctgcaaaattgttttgacgatatggtgcacattctgaagGAAGCACAAGAGTATGCAGAGAAGAATAATATGGTTTTCATCGAGACATCAGCAAAGACAGCTGATAATATAAACCAAGTATTTGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 7
------------gtagtgcaaca-ctatgtaatatagttgtcatataaacaaaataatcatttttttctcatatag-tatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
            |   |    || ||     |||| || || | ||       |  ||    | ||   ||||| | |||| | ||||  || || || |    |    ||||| |||||||||||   |||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||
gtaagagtatatgctctttgccaactgatagatattgtagtta-atggctgctactatatgatcttgaccatatggatatggtgtacttgttgcagGATGCGCAG----GACTACGCAGAGAAGAACAATATGTTTTTCATTGAGACGTCGGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G863105_T01 (Zea mays), 3'ss of exon 2
--------gtagtgcaacactatg--taatatagttgtcatataaacaaaataatcatttttttct-catatagt--atgctttactgtttccatgaagGATGGCACTG-ACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
           || |  |   | |       |    | ||  | || |      |||     | ||  || |  |  |   | |  |||     |   ||   |||| | ||||||||||||||||    ||||||||||| ||||| || || |||||||| |||||||||||  |||||||||||
gaccatggaccgtccggcctcagggccggactgtccgccagctcaaaatggcgctcaacaactgctatatgttattgacaatatggtgtacttgttgcggGATGCACAGGACTATGCAGAGAAGAACAAAATGTTTTTCATTGAGACGTCAGCCAAGACAGCTGATAATATAAACCAACTGTTTGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: AT3G54840.1 (Arabidopsis thaliana), 3'ss of exon 6
------------------gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgc--tttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
                   |    | | | |  |||    | || |  | | |     ||  || ||  ||  |||  | ||||    ||| |  ||||     ||||||| |  ||   |||||||||||| || ||||| ||||| ||||| || || |||||||| ||||| |||||| |||||||||||
gtgagtttgcgtaaacgtcttcatctagattccgtagcgcattt-tgttgtcactttcattgtccttgcttcttca-gtggtatcacattttcaatttcttaacagGATGGAATGGAGCTTGCAGAGAAGAACGGCATGTTCTTCATTGAGACGTCAGCCAAGACAGCCGATAACATAAATCAACTGTTTGAG

upper sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 6
gt-agtgcaacactatgtaatatagttgtc--atataaacaaaataatcatttttttctcatatagtatgc-tttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
|| ||||  | ||||| |     | |  |      |   | |  || |||     |   | | ||  | |  |||| | | | | |||||||||| | ||| ||||||||||||||||||||||| || || || ||||||||||||||||| ||||| |||||  | |||||||||
gtgagtgtcatactatttgtctgaatgcttcagcttttcctatgtattcacaaaatgtgc-tttaacacgtgtttattttattcttgaagGATGGTATTGATTATGCAGAGAAGAATGGTATGTTCTTTATTGAAACATCTGCAAAGACAGCTGATAACATAAACCAGCTGTTTGAG

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|151394915|gb|EV264786.1|EV264786
EST:     TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
EST: gi|192326781|gb|FK018908.1|FK018908
EST:     TGGTCGGTAATAAAGCTGATCTT-T-GAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
EST: gi|9900885|gb|BE609853.1|BE609853
EST:     GGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATACAGACATCT
genomic: GGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
EST: gi|298182667|gb|HO031402.1|HO031402
EST:     TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATG
genomic: TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATG
EST: gi|192296028|gb|FG989422.1|FG989422
EST:     TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
EST: gi|4277041|gb|AI431205.1|AI431205
EST:     TGGTCGGTAATAAAGCTGATCTTCTTGATAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT
EST: gi|151411846|gb|EV281657.1|EV281657
EST:     TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAG                         GATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATGGAGACATCT
genomic: TGGTCGGTAATAAAGCTGATCTTCTTGAGAAGCGGGAAGTTGCTGTCCAGgtagtgcaac ... ttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataaacaaaataatcatttttttctcatatagtatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG
                                         ctgtttcc  CT-rich tract
      aaaataatcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgcaacactatgtaatatagttgtcatataaacaaaataatcatttttttctcatatagtatgctttactgtttccatgaagGATGGCACTGACTATGCAGAGAAGAATGGTATGTTTTTCATAGAGACATCTGCAAAGACAGCAGATAATATAAATGAACTGTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT