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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGAACCATCTCAATCTGGTTCTTGTGAACAACGTGCCACTGTTTTTCAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagtttatagttcttgcatatttttacttgtctaatatattttgccggtttttaaggtgtattttgaatgcatagtgcataccttttatatgatgca...

Basic information

species Glycine max
transcript GLYMA04G41130.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G41130.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g21180.2 (Oryza sativa), 5'ss of exon 4
--TCAGAACCATCTCAATCTGGTTCTTGTGAACAACGTGCCACTGTTTTTCAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagtttatagttcttgcatatttttacttgtctaatatattttgc-cggtttttaaggtgt-attttgaatgcatagtgcatacc-ttttatatgatgca
   || || ||||| ||||| ||  | ||||| || || ||||||||||||| | |||||||||| || |||||||| |||||||| ||||| ||||  |||||  ||  |   |||    | |  |  | ||     |  | |  |  |  |||||| | ||| | |    |||  | |     ||| |||   || ||   
AGCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttctt--ctctcctttttcctggcatgaaatctgcactaagttctttttttatgatgttaatcattatgtgtgggctccaccatttcgcattatct-

upper sequence: GLYMA04G41130.2 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g21180.1 (Oryza sativa), 5'ss of exon 4
TCAGAACCATCTCAATCTGGTTCTTGTGAACAACGTGCCACTGTTTTTCAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagtttatagttcttgcatatttttacttgtctaatatattttgc-cggtttttaaggtgt-attttgaatgcatagtgcatacc-ttttatatgatgca
 || || ||||| ||||| ||  | ||||| || || ||||||||||||| | |||||||||| || |||||||| |||||||| ||||| ||||  |||||  ||  |   |||    | |  |  | ||     |  | |  |  |  |||||| | ||| | |    |||  | |     ||| |||   || ||   
CCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGTgtaattttctt--ctctcctttttcctggcatgaaatctgcactaagttctttttttatgatgttaatcattatgtgtgggctccaccatttcgcattatct-

upper sequence: GLYMA04G41130.2 (Glycine max), 5'ss of exon 4
lower sequence: Vv14s0060g01920.t01 (Vitis vinifera), 5'ss of exon 4
TCAGAACCATCTCAATCTGGTTCTTGTGAACAACGTGCCACTGTTTTTCAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagtttatagttc-ttgcatatttttacttgt-ctaatatattttgccggtttttaaggtgtattttgaatgcatagtgcatac-cttttatatgatgca
||| |||||||| ||||||||  | || ||||| |||||||||||||||| ||| || |||||||| |||||||| || || || ||||| || | ||||||||| | |  ||  |||  |||| |  ||| |  || || |  ||||   |||||      || |||     | | |    |   || ||  ||| ||  
TCAAAACCATCTGAATCTGGTGTTGGTCAACAATGTGCCACTGTTTTTCAATGTTCGGGATGGACCTTACATGCCTACATTACGACTTCTTCACCAATgtaaagtatttctttaattgtctattatatcttatgttattacaaattgc-aatttttgttaaataatttattgtcgtggattttctgctcttgcatgctg--

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|151410220|gb|EV280035.1|EV280035
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|58016274|gb|CX703016.1|CX703016
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|151395221|gb|EV265092.1|EV265092
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|298176588|gb|HO023175.1|HO023175
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|298176132|gb|HO015537.1|HO015537
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAACGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|10847978|gb|BF070551.1|BF070551
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|298173235|gb|HO020219.1|HO020219
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|151413172|gb|EV282980.1|EV282980
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
EST: gi|7795432|gb|AW780757.1|AW780757
EST:     CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTAT                         ATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG
genomic: CAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagttta ... ttttttgtagATCCAAATATAATGAAAAAGTTACAAGTTGACCGTGGTGCAATTAGATTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGAACCATCTCAATCTGGTTCTTGTGAACAACGTGCCACTGTTTTTCAGTGTCCGTGATGGACCATACATGCCCACCTTGCGTCTTCTCCATCTATgtaaagtttatagttcttgcatatttttacttgtctaatatattttgccggtttttaaggtgtattttgaatgcatagtgcataccttttatatgatgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA