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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattccctttccttttctcttatagcttctatctaatctaatatcaaaatttttacgtcttaactgttgatccatgctatgcgtag

Basic information

species Glycine max
transcript GLYMA20G33630.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G33630.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G069827_T03 (Zea mays), 5'ss of exon 4
ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattccctttccttttctcttatagcttctatctaatct-aatatcaaaatttttacgtcttaactgttgatc-catgctatgcgtag-------
||||  ||  ||||| | || ||||||||| | |||||||||||||||||||| || ||  | || |||||||||||| || |      | || |  |    || || ||  || |  || |    |||| |   || |        ||  ||   |||   |||       
ATGAATGCAATGAAGGCAGCAAACAAGGAGCTCAAGGGAATGATGAAAACTGTCAAAATTGATGAAATTGATgtatgtgttgctaccattcttgtgctcccactactttcagattttgatttatccatttctgattcattgtgaaaaatttcacaatattgctagatgagca

upper sequence: GLYMA20G33630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G04850.1 (Arabidopsis thaliana), 5'ss of exon 4
ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattccctttccttttctcttatagcttctatctaatct---aatatcaaaatttttacgtcttaactgttgatccatgctatgcgtag
||||||||  | || ||||| ||||||||| |||| |||||||||||||| || ||||| ||||| || ||||||||| ||   | |  ||    ||| |    | | | |  |      |||      |  ||| |  |||  |||||    || | |       
ATGACAGCGCTAAAATCTGCTAACAAGGAGCTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATAGATgtatgtcttggttcttattcaagcttctcttgtgtgtttgcttcctagatactgttttggttaagaattatttgttg---tataccacag----

upper sequence: GLYMA20G33630.1 (Glycine max), 5'ss of exon 4
lower sequence: AT3G10640.1 (Arabidopsis thaliana), 5'ss of exon 4
ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattccctttccttttct-cttatagcttctatctaatctaatatcaaaatttt---tacgtcttaactgttgatccatgctatgcgtag-----
||||||||  | || ||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||||||| ||  |    || |||  |  | | | | || |||||  | | |        | |    |  |  ||  ||| |  | |   ||||   | |     
ATGACAGCACTAAAATCTGCGAACAAGGAGTTGAAAGGAATGATGAAAACCGTCAAGATTCAAGATATTGATgtacgttgttaagttacttaacaacatcttggttttatcttgtttcaagcttttctctggtatttgatttgcctgatactacgatctattgatggtacag

upper sequence: GLYMA20G33630.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0007g02300.t01 (Vitis vinifera), 5'ss of exon 4
ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattccctttccttttctct-tatagctt-ctatctaatctaatatcaaaatttttacgtcttaactgttgatccatgctatgcgtag
||||||||||||||  |||| ||||||||||| || ||||||||||| |||||||||||  |||| || ||||| |||||| | || ||     ||| |  | | | ||| ||| | |   |||   |     |   || |||   ||||   |  | |    ||
ATGACAGCTTTGAAAGCTGCAAACAAGGAGTTAAAAGGAATGATGAAGACTGTGAAGATTGAAGATATAGATgtctgtattgctttaccgaggttctatgcatcatgctagcta-tatttcatctggaccgccaaa-ctgaacaactgattgtttttgttttcag

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|254320040|gb|GR830956.1|GR830956
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|298174856|gb|HO014773.1|HO014773
EST:     ACAAGGAGCTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAA
EST: gi|254325618|gb|GR838499.1|GR838499
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|298163684|gb|HO012417.1|HO012417
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|207790719|gb|GD761856.1|GD761856
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATTCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|15287713|gb|BI471604.1|BI471604
EST:     TTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: TTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|192326636|gb|FK018853.1|FK018853
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|151397618|gb|EV267491.1|EV267491
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|58024021|gb|CX710762.1|CX710762
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|298199136|gb|HO042499.1|HO042499
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAA
EST: gi|298176762|gb|HO023235.1|HO023235
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAA
EST: gi|254325619|gb|GR838500.1|GR838500
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|192314082|gb|FK010362.1|FK010362
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
EST: gi|192294647|gb|FG986496.1|FG986496
EST:     ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGAT                         AACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA
genomic: ACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattc ... ctatgcgtagAACTTGCAAGATGAGATGATGGACCTCATGGATGTAAGTAATGAAATCCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACAGCTTTGAAGTCTGCCAACAAGGAGTTGAAGGGAATGATGAAAACTGTGAAGATCCAAGACATTGATgtatgtattccctttccttttctcttatagcttctatctaatctaatatcaaaatttttacgtcttaactgttgatccatgctatgcgtag

- - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA