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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaaataataaaatctcgaattgccttaaattgatggcatgggtgagggtgattgcgaatttggcaccttatattagtggctgctactac...

Basic information

species Glycine max
transcript GLYMA13G00990.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 17
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 5'ss of exon 16
GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaa---ataataaaatctcgaattgccttaaattgatggcatgggtgagggtgattgcgaatttggcaccttatattagtggctgctactac
|  |||||| || || || | ||||||||| || |||||||||||||| ||||||||||| ||||||||  | |  || ||||| ||| | || || ||||||| | | |   |   || | | | |  |  ||    ||   || ||    |  || ||  |  ||  |   |       | |   |  |    | |||   
GGACATGATCTCCCAGGGTGGTTACATTTACGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCATTGTACAGGAACAGgtatttttctcacagccattacacacttgctgataaaatttgtttcattctgtccgtcagtatatttctggcataaattgatgacggttttttgcgttacag-

upper sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 17
lower sequence: GRMZM2G144407_T01 (Zea mays), 5'ss of exon 17
GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaaa-taataaaatctcgaattgccttaaattgatggcatgggtgagggtgattgc--gaatttg-----gcaccttatattagtggctgctactac--------------
|  |||||| || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||||||  | |  || ||||| ||| | || |||||||||   || ||     || |  || ||  ||      ||  |  |    ||   |  |  |  ||    | || ||     |   || ||   | || |  | | |                
GGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGATGCCAAAGGCATGGCCAGAGATGTACATAGAGTTCTCCACACCATTGTTCAGGAGCAGgtactgatcttaggcctagttgaaactttaaaaaaaatacttgcacactataaatatgcttctttctctgcatctgttgttgtttctcatgcaattgtcgacaatttttttttggcgaacag

upper sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 17
lower sequence: AC217947.4_FGT002 (Zea mays), 5'ss of exon 16
GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaaa-taataaaatctcgaattgccttaaattgatggcatgggtgagggt--gattgcgaatttggcaccttatat-tagtggctgctactac----------
|  |||||| || ||||| |||||||| ||||| |||||||| ||||| ||||||||||| || |||||  | |  || || || ||| | || |||||||||   ||  |     || |  || ||  ||     | |  | |||   || | || |  |     |  |  | ||     |   ||  | | |  | || |            
GGACATGATCTCCCAAGGTGCTTACATCTATGTCTGTGGTGACGCCAAAGGCATGGCCAGAGACGTACATAGAGTTCTCCATACCATTGTTCAGGAGCAGgtactgatcctaggcctagttcaaacttaaaaaaaat-acttagatactatagatgtgcttctatctctgcctctgctgtttctcatgcatttgtcgatatttttggcaatcag

upper sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 17
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 5'ss of exon 16
GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaaataataaaatctcgaattgccttaaattgatggcatgggtgagggtgattgcgaatttggcaccttatattagtggctgctactac
||  ||||| ||||||||||||||  | ||||| |||||||| ||||| |||||||| || ||||| ||| |  | || ||||||||    ||||| ||||||| | || || |   || || ||| | |||  | |     | |  ||            | || |  | |  |    | | ||  |  | |       
GAATATGATCTCTCAAGGAGCTTATTTATATGTTTGTGGTGACGCCAAAGGCATGGCAAGAGATGTTCACAGATCTCTCCACACAATAGCTCAAGAACAGgtatgtcttgttgag--atcaa-tctagcattatcattgtccg-tatcacaaaccgactctaatgagtttatttctgtctgtcttgttttcag-------

upper sequence: GLYMA13G00990.1 (Glycine max), 5'ss of exon 17
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 5'ss of exon 17
GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaaataataaaatctcgaattgccttaaattgatggcatgggtgagggtgattgcgaatttggcacc-ttatat-tagtggctgctactac-----
||   | || ||||| ||||  ||||||||||| |||||||||||||| |||||||| |||||||| ||| |  | || || || || |||||||||||||||  |   |  ||||||   ||||   ||   || | ||| ||    |||| ||    |   | |     ||  | | | |||  || ||  | | || ||     
GAATGTAATTTCTCAGGGAGGCTACATTTATGTCTGTGGTGATGCCAAAGGCATGGCAAGGGATGTCCACAGAACTCTTCATACCATCTTGCAAGAGCAGgtacgttcatacaaataa---aatc---aacatccctgaatcgacaa-atggctgcctctacctaccttgatgaaatcatcatacctaatgtttaccaccacccatt

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|308098963|gb|HO760804.1|HO760804
EST:     ACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: ACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209728345|gb|BW659982.1|BW659982
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209722908|gb|BW669454.1|BW669454
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAAATTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|254318721|gb|GR828665.1|GR828665
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209729002|gb|BW655032.1|BW655032
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|6914702|gb|AW396232.1|AW396232
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209699334|gb|BW664053.1|BW664053
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|213612147|gb|DB976808.1|DB976808
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACTCTTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209727361|gb|BW663346.1|BW663346
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209728635|gb|BW660250.1|BW660250
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|213593099|gb|DB975346.1|DB975346
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GTTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAAAAC-ACAAAC
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAG-AATCTACAAAC
EST: gi|209710559|gb|BW670983.1|BW670983
EST:     GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: GCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
EST: gi|209709241|gb|BW678660.1|BW678660
EST:     CCCTGCACACAATTTTGCAAGAGCAG                         GGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT
genomic: CCCTGCACACAATTTTGCAAGAGCAGgtatatattt ... atcatatcagGGTTCTCTCGATAGTTCCAAGGCTGAGAGCATGGTAAAGAATCTACAAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGCATGATATCTCAAGGAGCTTACATTTATGTGTGTGGTGATGCCAAGGGCATGGCCAGGGATGTACACCGTGCCCTGCACACAATTTTGCAAGAGCAGgtatatatttttaaataataaaatctcgaattgccttaaattgatggcatgggtgagggtgattgcgaatttggcaccttatattagtggctgctactac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgagg