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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG

Basic information

species Glycine max
transcript GLYMA08G43590.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g56980.1 (Oryza sativa), 3'ss of exon 2
---------gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggt------tttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG
         | ||   || ||  | ||  ||    | |  | |  |||  |    | ||||| | | |  |  ||     |  | |     |||||||    |      || ||||||| ||||| || |||   || ||  || |||| ||||| ||||||||     |||||||||| ||||| |||||||||||||| |||||||| ||||
gtaatctcagctttccccaattgtattagagaaaatggcatcc--aatttaatcctgtgataaactctttaatgaatcaaccgagaca--aagtaacttgcttcctccattcagATTGTCAAGCAGCTTTGGCAATATATTCGGCAGAATAATCTTCAAGATCCTGATGACAAAAGGAAGATAATCTGCAATGATGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G124502_T01 (Zea mays), 3'ss of exon 2
--------gtttgtaccgatattt-ttgaagcttgttgtttgcttaatgcataattttgat-atagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG
         ||  |   ||||    || |  |    |||   |||   | |   |||  || || |  || |  ||| | |  |||||    | ||    |  ||  ||||||||||||| || ||||| || || ||| |||||||||| ||||||||     |||||||||| || ||||||||||| ||||| |||||||| ||||
gtactaaatttcattgtgatagaaatttacacactctgtactcttctggtactctttgaatgattgactctatagag-tctagaaaataaatattagtctttattc-agATTGTGAAGCAGCTCTGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATTATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G035325_T01 (Zea mays), 3'ss of exon 2
gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattt--tgatatagtttcca-gcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG
  |  |||  |  || || |   | |   ||  |  | |  ||| | |  || ||   |||  | |   || |     ||  |   || | | |   || ||||||||||||| || ||||| || || ||| |||||||||| ||||||||     |||||||||| || ||||||||||| ||||| |||||||| ||||
-gtactactcaatttctttacaatagaaattgacacactctatactctactggtactctttgaatgattgactctaggaaattaatgttagtcttcattcagATTGTGAAGCAGCTATGGGCATATATCAGGCAGAACAATCTTCAAGATCCTGATGACAAAAGGAAGATCATTTGCAATGACGAACTTCGTGTGGTTTTTG

upper sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G22360.1 (Arabidopsis thaliana), 3'ss of exon 2
gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG
     || |  | | ||| |   ||  || ||      || ||||      | | |||   |   |  | |      ||||       | |||||||||||||||| |||| |||||||||| ||||||||||| || || ||||| || || |||||  |||| || || ||  ||||||   |||||||||| ||||
---gttatcattgtctttca---tttatgattataatgtgtataagca-attgtggttgttatttatgtgtt---gctgtgtttggcttttggttttagATTGTGAGGCAATTGTGGGCTTATATAAGGAAGAATAACCTTCAAGACCCGAGTAACAAGCGGAAGATCATCTGTGATGATGCGTTGCGTGTGGTTTTTG

upper sequence: GLYMA08G43590.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv19s0090g01460.t01 (Vitis vinifera), 3'ss of exon 2
------gtttgtaccg---atatttttgaagcttgtt-gtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG
       || |||      ||||  || | | ||||| |   | || ||      |  | ||||  ||  || | | ||||| || ||||          | | || |||||||||| || || ||||| ||||||||||  ||||||||||||||||| || ||||||||||| ||||||||||| ||||| || ||| |||| ||||
gttcagattcgtaaaagatatatccttaacgattgtttgccagttttatatcatttcctaatattattggcatcta-atttccaatatgt----------ttggttcagATTGTGAAACAGCTCTGGGCATACATAAGGAGAAACAATCTCCAAGATCCAAGTAACAAAAGGAAGATAATTTGCAACGATGAGCTACGTTTGGTATTTG

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|208320218|gb|GE122919.1|GE122919
EST:     CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAG                         ATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
genomic: CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAGgtttgtaccg ... gtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
EST: gi|33388029|gb|CA851236.1|CA851236
EST:     CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAG                         ATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
genomic: CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAGgtttgtaccg ... gtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
EST: gi|16996625|gb|BM085997.1|BM085997
EST:     CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAG                         ATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
genomic: CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAGgtttgtaccg ... gtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
EST: gi|9258697|gb|BE346844.1|BE346844
EST:     CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAG                         ATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC
genomic: CGCCTGAACTTCAGGTCATTGTTGGCCAGCCAGCATTGTCGAGGACTGAGgtttgtaccg ... gtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgatatagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG
                                     gagtaac  putative branch site (score: 2)
                       atttctaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaccgatatttttgaagcttgttgtttgcttaatgcataattttgatatagtttccagcgagatttctaaaatgtggagtaactgtggttttagATTGTGAAGCAACTGTGGGCTTACATAAGGAAGAACAATCTCCAAGATCCCAGCAACAAAAGGAAAATAATTTGCAATGATGAACTGCGTGTGGTGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA