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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcattccattggcctgccctgtcctggattcttatcatgctacagattgcatgtgaaataaaaatataaattcttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG

Basic information

species Glycine max
transcript GLYMA07G03890.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 21
-------ctcattccattggcctg--ccctgtcctggattct-tatcatgctacagattgcatgtgaaataaaaatataaattct-tatatttagttgttaata-tgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
       || | ||   ||  ||   |  ||   || |   | |       | ||||   ||| |    | |   |     || | | |||| |  ||||  |  || ||||||||||||||||||||| || ||  |||| ||||||   || ||||| ||||| ||||| || ||||| ||||||||  |||| |||   || | | |  
gtaatttcttaatcttctgctcttatctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacagGTTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAGTATCCAAATTTATTTGAAGACTGGCAGGTTGCACTTACTGTAGAAAAGAATGTTGCTT

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
ctcattccattggcctgccctgtcctggattcttatcatgctacagattgcatgtgaaataaaaatataaatt-----cttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
                    |    |  | |||| | | | |  ||  |  |||||    ||  | | || ||      |||  ||   |||    |    |||||||||| ||||||| || ||||| ||||||||||||||||| ||  | ||| | ||||| |||||||||||||| ||  |||| ||| ||||||||   |
------------------gttcctttcaaatctttttaggttttagtgta-atgtggt-caaggagacaagttgtgggtttaagttaccttgcacttgaatacagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 21
ctcattccattggcctgccctgtcctggattcttatcatgctacagattgcatgtgaaataaaaatataaattcttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
                |   | | |     | || |     ||| |  |  ||| ||||    |  ||      ||| |||   ||     | |   ||||||||||||||||| |||||||| || ||||||||||| || ||  | ||| | ||||| |||||||||||||| ||  |||||||| | ||  || | |
----------------gttattttcgcatcttttttttgtttactgtgtcaatgagaaaattcatcatgtggctttaaattgcctttgacttgtcatcagGTTAATCCAAAAGCAGCTGAATCTTTAGCTGATCCTGAAGAGTACTCAAATCTTTTTGAGGATTGGCAAGTTGCTCTTTCTGTTGAAGCGAACACTGCAG

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 21
ctcattccattggcctgccctgtc--ctggattcttatcatgctacagattgcatg--tgaaataaaaatataaattctta----tatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
        ||  ||||||   |     |||||   | ||||   ||   |    ||  | ||| ||| | | | ||   ||    | |||  |    | |||   |||||||||||||||||||||||||| |||||||||||||| || ||||||||||| ||||| || ||||||||||  || ||  |||||||||||| | | |
--------atatgcctgcttgggtagttggatctatttcatttaacttttcttgtgatttaaagaaagagacacatatctaatcctgtttgatcaacactatatgcagGTTAATCCAAAAGCTGCTGAATCTTTGGCTGATCCTGAAGAGTATCCTAATTTATTTGAGGACTGGCAAGTTGGTCTTGCCATTGAATCTAAAGTTGCCG

upper sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
ctcattccattggcctgccctgtcctg-gattcttatcatgctacagattgcatgtgaaataaaaatataaattcttatattta-gttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
  |||  |||       ||  |    | |||    |  | |  |  || || |  |     |    | |  | |     ||  | | ||| |  ||   ||||| |    ||||||||| ||||||||||| |||||||| || || |||||||||||||| || ||||| ||||| || |   |||||||||||  | | |
--catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatgatttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG

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|10231240|gb|BE800056.1|BE800056
EST:     CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG                         GTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAAT
genomic: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatttgtt ... atatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAAT
EST: gi|298182438|gb|HO026613.1|HO026613
EST:     CAAGCAAGGTCTCGGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAG                         GTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCCGAGGAATATCCTAAT
genomic: CAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatttgtt ... atatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgcatgtgaaataaaaatataaattcttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG
                                        tgttaat  putative branch site (score: 3)
           aaataaaaatataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcattccattggcctgccctgtcctggattcttatcatgctacagattgcatgtgaaataaaaatataaattcttatatttagttgttaatatgcacagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAGGAATATCCTAATTTGTTTGATGATTGGCAAGTTGCACTAGCTGTTGAATCTAAAGCTACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT