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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA

Basic information

species Glycine max
transcript GLYMA08G15340.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G013750_T04 (Zea mays), 3'ss of exon 4
gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgt---aactaattagtattcagtttacttatggaatgggtaatctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
 | |     ||  |   ||  || ||  |   ||  ||| |||  | ||   |      || || | ||    ||    |       ||   |  || | | ||||| |||||||| ||  ||||||| ||||| ||||||||||| ||||||||||| || 
-tgaaccctaa-atactacg-gtattcataaattccatagttttatcttgaaactccaaaaatactgagctaccaaaacaggccct-aacaagctattt-atcagGTCGAAACATTTGGCTCCATGGCAAAGACGGAGAAAATTGCTTTCATTCTTGAGCAG

upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtgtgaatgtgtcacatgttttgttggctt--gtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
    ||  |  | | |  |     ||     |||  ||  |  | |||||||  || ||  | ||   |  ||| | | | |      ||  ||      | ||||||| ||||| ||||| ||||| || |||||||||||||| |||||||||||||||
----gtaagcttttcttcctctactttccaactttcgtggaaatcgtttttt--atttattttatagtttatcaatgtgcattgattgtgattatgaattatagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCTTTCATTCTTGAACAA

upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
              || | ||  |||||    |||  || |   | |  ||||  |          | || |        ||   ||   ||||   |||||||||| ||||| ||||| ||||| || |||||||||||||| || || |||||||||
--------------gtaagat--tttgtgcatttggctattaaatctcctggaaattttcttcccttgttaacccctgcaatttgataaataatt--aacagGTGGAGACATTTGGTGCTATGGCAAAAACTGAGAAAATTGCATTTATCCTTGAACAA

upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 4
gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagtattcagtttacttatggaatgggtaatctga----------------acagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
|||||| | ||  |   | |  |    | ||||| |    |||| | || | |   |   |    ||  |  ||||   |||   | | | | | ||                 ||||||||||||||| ||||| ||||| || ||||| |||||||| |||||||||||||||
gtcagt-taaaaat---agagttaccatgggctttttatttttggtattagaaaacactaaccccgttgtttgtttttatattacacgagcactttggttgatgttacttaatcacagGTGGAAACATTTGGTGCAATGGCAAAAACTGAAAAAATTGCATTCATTCTTGAACAA

upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S58_256V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------gtcagtgtgaatgtgtcacatgttttgttggcttgtatactttgttttttggatgtaactaattagt--attcagtttacttatggaatgggtaatctga-acagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
                                                                        ||| ||||||| |||  |   | |   |   |  ||| |  ||| | |  | |  |  ||||||  |  |     | || | |||       || ||  |   ||||||| || |||||||| ||||| ||||| ||||||||||| |||||||| || || 
gtatgatccctaatcttccactttttttgaaacttatatttaggagcaagaaatttcgtttttgatctcgaagtcggtgtgaa-gtggtatgcggtgcctgaaccagtaga--ttggtctacgcagctttctaattgatgcacctgatctaataatgttgcaa-tactccaatgaagGTGGAGACCTTCGGTGCTATGGCAAAGACAGAGAAAATTGCTTTCATTCTAGAGCAG

upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S257_89V6.2 (Physcomitrella patens), 3'ss of exon 4
--------------------------gtcagtgtgaatgt--gtcacatgttttgtt---ggcttgta---tactttgttttt--tggatgtaactaattagtattcagtttacttatggaatgggtaatctgaac-----------agGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
                           ||| |   |  ||  || ||||||  ||||   ||  || |    | |||| |  |  | ||    ||    | || |   |  || |   |   ||  |  | |   |           |||||||||| || ||||||||||| || |||||||| ||||| |||||||||||||||
gtatgtgatattgcttcgtgctgttgatcaattcaacggttagtaacatgtaatgttcatggtgtggaagacattttggtgctactagagtgcacagggtggtgtattgaatattggagccctgattcgtatcggcgtttggtcttcagGTGGAAACTTTTGGTGCCATGGCAAAAACTGAGAAGATTGCTTTCATTCTTGAACAA

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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggatgtaactaattagtattcagtttacttatggaatgggtaatctgaacagGTGGAAACATTCGGTGCCATGGCCAAGACTGAGAAAATTGCGTTCATTCTTGAACAA
         aactaat  putative branch site (score: 2)
        taactaattagtatt  TA-rich tract