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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGGAAATTGAGAGAGCTCGATTGATCAAAAAACTTGCAAAGATTAAGGAAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacag

Basic information

species Glycine max
transcript GLYMA08G15340.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 5'ss of exon 4
CGTGGAAATTGAGAGAGCTCGATTGATCAAAAAACTTGCAAAGATTAAGGAAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacag
 || ||||| ||||||||||| |||| ||| |  ||||| ||||||||||||||||||||  | || ||||||||||| ||| | ||||||||| |||| || ||  |   |   ||   | |     |   | ||  |  | |||||||  || ||  | ||   |  ||| | | | |      ||  ||      | ||
TGTCGAAATCGAGAGAGCTCGTTTGACCAAGATGCTTGCTAAGATTAAGGAAGAACAAGGTTTGATTGCTGAAGCTGCGGATCTCATGCAAGAAGTTGCTgtaagcttttcttcctctactttccaact--ttcgtggaaatcgtttttt--atttattttatagtttatcaatgtgcattgattgtgattatgaattatag

upper sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 5'ss of exon 4
CGTGGAAATTGAGAGAGCTCGATTGATCAAAAAACTTGCAAAGATTAAGGAAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacag
 || ||||| ||||| || ||  | | ||| |||||||| ||||||||||||||||| || |  |||||||||||||| ||| | ||||||||| |||| || ||  |   ||  |       ||   |  | || | | ||| ||   | | |    |     | |    |  | | | |  |                  
TGTTGAAATCGAGAGGGCACGTCTCACCAAGAAACTTGCTAAGATTAAGGAAGAACAGGGTCAGATAGCTGAAGCTGCAGATCTTATGCAAGAAGTTGCTgtaagattttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacccctgcaatttgataaataattaacag------------------

upper sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 4
CGTGGAAATTGAGAGAGCTCGATTGATCAAAAAACTTGCAAAGATTAAGGAAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacag----------------
 || ||||| ||||| |||||  ||||||| ||||| ||||| || |||||||| ||||||| ||||||||| || |||||||||||||||||||||||||||||| | ||  |   | |  |    | ||||| |    |||| | || | |   |   |    ||  |  ||||   |||   | | | | | ||                     
TGTTGAAATAGAGAGGGCTCGGCTGATCAAGAAACTAGCAAAAATAAAGGAAGAGCAAGGGCATATAGCTGAGGCAGCTGATTTGATGCAAGAAATTGCGgtcagt-taaaaat---agagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacag

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|14990252|gb|BI315925.1|BI315925
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|308097990|gb|HO761161.1|HO761161
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|308098358|gb|HO760099.1|HO760099
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|308098130|gb|HO761301.1|HO761301
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|192296110|gb|FG989470.1|FG989470
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|6566939|gb|AW234570.1|AW234570
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|15286081|gb|BI469972.1|BI469972
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|192334269|gb|FK024396.1|FK024396
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|19054166|gb|BM732833.1|BM732833
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|26057523|gb|CA800437.1|CA800437
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|18734293|gb|BM528099.1|BM528099
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|15284757|gb|BI468648.1|BI468648
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
EST: gi|12690044|gb|BG156380.1|BG156380
EST:     AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCG                         GTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT
genomic: AAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtga ... atctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGGAAATTGAGAGAGCTCGATTGATCAAAAAACTTGCAAAGATTAAGGAAGAACAAGGGCTTATAGCTGAAGCTGCTGATTTGATGCAAGAAATTGCGgtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA