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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttgttgtctcattacttaaattcatctaatttcaattttttttaattgcaattgctatgctatagaacattaaactaatatctctcactatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG

Basic information

species Glycine max
transcript GLYMA05G30830.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 12
gtgagtttgttgtctcattacttaaattcatctaatttcaattttttttaattgcaattgctatgctatagaacattaaactaatatctctca--ctatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG
              |  | || ||  |    ||| ||  |||  | |   |||     |    |   ||  |  || | | |   |  ||     || | |   ||||||||||||||||||||||||| || |||||||| |||||  ||||||||| ||||||||| || ||||| |||
-------------gtactgacctatgtctgcctacttctaatactctcatattatttgtttgttagcatgcatgatcatattggaacttcctcgtctttgaaacagCCTGCCCATGAGAAAATTGGAGTCGTAGATTCTCAATGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 7
gtgagtttgttgtctcattacttaaattcatctaatttcaattttttttaattgcaattgctatgctatagaacattaaactaatatctctca--ctatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG
              |  | || ||  |    ||| ||  |||| | ||  ||      |    |   ||  |  || | | |   |  ||     || | |   |||||||||||||||||||||||||||| |||||||| ||||| |||||||||| | ||||||| || ||||| |||
-------------gtactgacctatgtctgcctacttctaattctcttatatcatttgtttgttagcatgcatgatcatattggaacttcctcgtctttgaaacagCCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAATGGATCATTCATCAAACTTTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0106g00570.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtttgttgtctcattacttaaattcatctaatttcaattttttttaattgcaattgctatgctatagaacattaaactaatatct-ctca-ctatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG
              |  | || ||  |    ||| ||  |||| | ||  |||     |    |   ||  |  || | | |   |  | |||  || | |   |||||||||||||||||||||||||||| ||||||||  ||||  ||||||||| ||||||||| || ||||| |||
-------------gtactgacctatgtctgcctacttctaattctcttatattatttgtttgttagcatgcatgatcatattggaacttgctcgtctttgaaacagCCTGCCCATGAGAAAATTGGAGTTGTAGATTCTCAAGGGATCGTTCATCAAACTGTTCCCTCGCTTGGGAACCAG

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S70_58V6.1 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------------------------gtgagtttgttgtctcattacttaaat-tca-tctaatttcaattttttttaattgcaattgctatgct--atagaacattaaactaata---tctctcactatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG-------------------------
                                                                                         |||   || || |||  |   | || | ||| |||  ||   ||||| |     |     ||   || |  |||   |||  |   |||    | |||   |    || ||||||| ||||| |||||||||||||| ||| ||||||||||    ||||    ||| |  || |||   |    |                         
gtaagtttatacgaagttgaatttcgtcagtcgtaggtgcagagcttacataactttctaattgcatcaacaaatggacacaagcttcggtggacttctt-tctactagttgaagtatcactctggttgttattttctcagtctctgtctgaattgttggatatctcatctactgaatggtttgtcttgatgatttgcagCCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCGGTTTGTGTTCCTCACAACCATTCAC

upper sequence: GLYMA05G30830.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S70_58V6.2 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------------------------gtgagtttgttgtctcattacttaaat-tca-tctaatttcaattttttttaattgcaattgctatgct--atagaacattaaactaata---tctctcactatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG
                                                                                         |||   || || |||  |   | || | ||| |||  ||   ||||| |     |     ||   || |  |||   |||  |   |||    | |||   |    || ||||||| ||||| |||||||||||||| ||| ||||||||||    ||||    ||| |  || |||   |    |
gtaagtttatacgaagttgaatttcgtcagtcgtaggtgcagagcttacataactttctaattgcatcaacaaatggacacaagcttcggtggacttctt-tctactagttgaagtatcactctggttgttattttctcagtctctgtctgaattgttggatatctcatctactgaatggtttgtcttgatgatttgcagCCTGCACATGATAAAATTGGAGTTGTAGATGCTCAGTGGATCCGACATCGGGTTGTGCTATCTCTAAATAGCTCG

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|10256404|gb|BE824170.1|BE824170
EST:     ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
genomic: ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtttgt ... tatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
EST: gi|207713488|gb|GD696171.1|GD696171
EST:     ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
genomic: ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtttgt ... tatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
EST: gi|13312427|gb|BG406078.1|BG406078
EST:     ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
genomic: ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtttgt ... tatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
EST: gi|7146333|gb|AW508255.1|AW508255
EST:     ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
genomic: ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtttgt ... tatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
EST: gi|193459553|gb|FK423410.1|FK423410
EST:     GGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
genomic: GGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtttgt ... tatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
EST: gi|14009195|gb|BG725799.1|BG725799
EST:     ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAG                         CCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA
genomic: ATTTGGTCCATGGCTGGGGCCTTGATTTTGCTCTTAGAAAATGTGTTGAGgtgagtttgt ... tatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgcaattgctatgctatagaacattaaactaatatctctcactatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG
                                     tctctcact  CT-rich tract
                 tatagaacattaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttgttgtctcattacttaaattcatctaatttcaattttttttaattgcaattgctatgctatagaacattaaactaatatctctcactatcatgtagCCTGCCCATGAGAAAATTGGAGTTGTTGATTCTCAGTGGATTATTCATCAAAGTGTTCCCTCACTAGGGAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA