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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaatattcaggccatttatatgtcatttagtatatctacatcccaactcatcaaacaatctcccctacag

Basic information

species Glycine max
transcript GLYMA13G39210.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G39210.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 5'ss of exon 3
GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtata--caatattcaggccatt-tatatgtcatttagtatatctacatcccaactcatc-aaacaa--------tctcccctacag----
|||||||| |||||||||||||| ||||||  |||||| |||||||||||||| |||||||||||  | ||  | || || |||||||| ||||||||||||||   | || |  ||   ||   | ||    | |||  ||   |    | | || ||  ||||||        | |||  |   |    
GAGGAGGCGAACAATGCACATTACAATTCAGTAGCCATTATTGATGCTGATGGCACTGATCTTGGCCTGTACCGCAAATCACATATTCCAGATGGACCAGgtattgcccatgtatagtttatgacagattcactatagactagtcatggactatctgatttaaacaagttagctatttcctttttggctag

upper sequence: GLYMA13G39210.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G073950_T01 (Zea mays), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaatattcaggccatttatatgtcatttagtatatctacatcccaactcatcaaacaatctccccta--cag
|| || |||||||||||||||||||||||    || || || |||||||||||  ||||||||||  | ||| | || || || ||||| |||||||||||||      ||  ||||  ||  | |          ||      ||| || || || || |    ||   |   |||
GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaaggtcaat--aggcttttcctgttctgccatacattgggttatctcatct-ataaagccgcttctgtttgtcag

upper sequence: GLYMA13G39210.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaatattcaggccatttatatgtcatttagtatatctacatcccaactcatcaaacaatctcccctacag--
||||||||||| | ||||||||| ||||| |  || |||||||||||||||||||||||  | || |||||||| |||||||||||||| |||||||| |||     |  ||  |    |  | || |   ||    |   |    ||    |  | | ||    |    |      
GAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCTGATGGAACTGACTTGGGAATTTATAGGAAGTCTCATATTCCTGATGGACCTGgtgagtcaagtttggagt-tggaaatatagcttgagtttcttgttacctttttgctgagacctctttttatcttaag

upper sequence: GLYMA13G39210.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaatattcaggccatttatatgtc-atttagtatatctacatcccaactc------atcaaacaatc-tcccctacag
|| |||||||||||||| ||||| |||||||  |||||| ||||||||||||| ||||||||||| || || |||||||| ||||| || ||||||||||||||   |   | |||  | | ||||  | |  | |||| | | |   |||  |       |  ||| | |  |  | |||||
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatact-atataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag

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|14125523|gb|BG789961.1|BG789961
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
EST: gi|15199519|gb|BI423872.1|BI423872
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
EST: gi|15813986|gb|BI786261.1|BI786261
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
EST: gi|209726298|gb|BW659611.1|BW659611
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
EST: gi|7924791|gb|AW830817.1|AW830817
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAN                         GTTACGAGGAANAGTTCTATTTTAATCCAAGTGACACTGGATTTAANG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAA-G
EST: gi|298165233|gb|HO011282.1|HO011282
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
EST: gi|193588755|gb|FK541357.1|FK541357
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATT
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATT
EST: gi|19935096|gb|BQ080126.1|BQ080126
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
EST: gi|209726043|gb|BW672766.1|BW672766
EST:     TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAG                         GTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG
genomic: TGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaata ... tcccctacagGTTACGAGGAAAAGTTCTATTTTAATCCAGGTGACACTGGATTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaatattcaggccatttatatgtcatttagtatatctacatcccaactcatcaaacaatctcccctacag

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