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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

Basic information

species Glycine max
transcript GLYMA07G01440.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
------------------------------------------------------------------------ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                                                        |||  |            |   |      ||| || |  | | || | | | ||   || ||         ||  | | | || |  |   | |  |||||||||||||||| ||||| ||||| ||| |||| || || |||||||| || || ||||| || || |||||||||   | |||||||||||| || |||
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatact-agtaatagaatgtcaca-atatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G142334_T02 (Zea mays), 3'ss of exon 8
---------ttttgcatacaaagaaaagcatttttctggatcctattatatttat----------tcatttatgtgatttcttttgcggtagactcacagaaa--attattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
         | || || || || | |  | | |   ||||   ||| |  |  ||          ||| ||||   ||   ||| |  |||   |  |   |    || | |||| |  || |||||| | || || ||||| || ||| ||||||||||||| |||||||| || ||||| || ||||||||||||  ||||||||| ||  |||| || 
gtgagcttttatttcacactaacatatac-tctacttggagaatatcaagtgaatactgcccttctcaattatcctataagtttcgttgtactatttctatacctgttgtcttct-tgtagCTTTGAGCAGCATGAGGCCCCAGGTTCAAGATCATTTTTCACTGAGATTATAGCTTCAATTTCGGACATAAAATTTTCGAAGGATGGGAGGCATATTCTC

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G164185_T02 (Zea mays), 3'ss of exon 8
---------------------------------------ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattat-tttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                       ||  | ||||        |    | |  ||    || |    |||| || ||||   |    |||    |||   | | |     | || | |   |  || |||||| | || || ||||| || ||| ||||||||||||| |||||||| |||||||| || |||||||| |||  ||||||||| ||  || | || 
gtgagcttttagtttacactttttatttcctacaatatgttcagtatactctacttggagaatattgggtggatactgaccttat-caattatcctaaaagtttccttgtatttttatacctgttcatgtcttcttgtagCTTTGAGCAGCATGAGGCCCCAGGCTCAAGATCATTTTTCACTGAGATTATAGCCTCAATTTCGGACATAAAGTTTTCGAAGGATGGGAGGCATCTTCTC

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G069631_T01 (Zea mays), 3'ss of exon 8
----------------------------------ttttgcatacaaagaaaagcat---ttttctggatcctattatatttattcattt-atgtgatttcttttgcggtagactcacagaaaattatt------ttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                  | |||  || || | || || |   |||| |   | ||| |   |  |  ||||| | ||   ||  || |   | | || |       | | |      |  ||| |||||||||||| || ||||| ||||| ||| |||| ||||| |||||||| || || ||| | ||||| ||||||||||  | |||||||||| | || |||
gttagtaaccccccttgaacttcagtaacattattgttgattagaaggcaatgcttagattttatcatttctaatggctacaaacattttaagtttatttattggtcatggtcttatctggtttaactggggcatcttgttcagATTTGAGGAGCATGAAGCACCTGGATCAAGATCCTTTTTTACAGAGATAATAGCATCAGTTTCAGATATAAAATTTGCAAGGGATGGAAGACACATTCTT

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
ttttgcatacaaagaaaagcatttttctggatcctattatatttattcat-ttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
  | |   || |||         | | |  | | |||  || | ||| || ||     | || || |  | |  |       | ||     |     |||||||||||||||| ||||| ||||| ||| |||| || || ||||| |||||||| ||||| || || ||||| |||   | | |||| | |||||| |||
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaa-acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
----------------------------------------------------------------------ttttgcatacaaagaaaagc-----atttttctggatcctatt--atatttattcatttatgtgatttcttttgcggtagactc-----acagaaaattattttctg----tacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                                                                       | || ||||   |           ||||||||   | ||  |    | | | |     |||    ||  |  ||   ||  ||     || ||  ||| ||   |      |||||||||| ||||  ||||| ||||| ||| ||||||||||||||||||| ||||||||||| ||||| || |||||    |||||||| ||||| ||||||
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

upper sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
---------ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
             | | |  || ||||  ||  || || |    |   | |||||| |     ||| | | |  ||    ||  |||  || | |    ||   | ||| |||||||||||||| || ||||| ||| ||||||||||||||||||| ||||||||||| |||||||| ||||||   ||||||||||||| |||||| 
tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttattta-----gtgctctttcctggatcag--tcagtgatagta--cttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

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|22525826|gb|BU084637.1|BU084637
EST:     CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACT                         ATTTGAGGAACAAGAAGCCCCT
genomic: CGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagctatc ... ttctgtacagATTTGAGGAACAAGAAGCCCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
                           gactcac  putative branch site (score: 2)
                                        ttattttct  putative PPT
                                    aaaattattttctgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - gcataca
- - - - - -aagaaaa
- - - - - - - - - - - -tttctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actcaca