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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgtatttgctaacatatttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

Basic information

species Zea mays
transcript GRMZM2G028037_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
gtaagcaactatattgaa----------atgttaaaaatattcattcatacaaatgtatt-------tgctaacatattt-ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
||| ||||| || ||  |          || ||| |||| |||||| | |       |||       | || | |||||  |||||||||||| || ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||| | ||||||||||| ||||||||||
gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 4
gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgtatttg-ctaacatattttt--ttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
    | || | |    || |   | ||   | ||||    |   | |||  | |||| ||  |     ||||||| || || || || ||||| |||||||| ||||| |||||||| || || ||||||||||| |||||||| ||| | || |||||||| ||||| ||||
----gtaagtgtcaaaaactacaataagattgcatttccccctttttatcagtctaatattgtaccgattcagGAGTACAATGCCAAGCTCTCAGATTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4
----gtaagc-aactatattgaaatgttaaaaatattc---attcat------acaaatgtatttgctaacatattt-ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
    || ||  ||| |     ||   ||  || ||||    || |||      ||| |   |  |   |||||| || |||| |||| || || || |||||||||||||||||||| || |||||||| ||||| || || || |||||  | ||||| || ||||||||||||||||| ||||
gtatgtgagttaaccaggaaaaaggtttttaattattttttatccatcctccaacataaaaacataaaaacataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G02480.1 (Glycine max), 3'ss of exon 3
-----------------gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgtat-ttgctaacatatttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
                 | |        |||   ||| || || ||||  || | | ||     || ||  || ||| | | |||||| |||| ||||||||||| || |||||||| ||||| |||||||  || | ||| |||||||  ||||| ||||| |  || ||||||||| | || ||||
gtaatagcttgaacattgcatttcttactatgataattttcaacatatatataccttcattgacatcttaataccat-tctgtttcagAACTACAACGCAAAACTTTCCGATTTTGGGCTTGCAAAAGATGCTCCAGTGGGAGATAAAAGCCATGTATCAACAAAAGTGATGGGAACAAAAGGGTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5
gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgtatttg-ctaacatattttt-------ttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
|||||   | |  || ||||  | |  || ||  ||   |    |  |||||  | | ||||| ||       ||||||| || || || || ||||| || ||||||||||| |||||||| || |||||||||||||| |||||||| ||| | || |||||||| ||||| ||||
gtaagtgccaaattttaaattattaccatttttcttttcattccttgatttgatttatatattattataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 4
gtaagcaacta--tattgaaatgttaaaaatattcattcatacaaatgtatttgctaacatattttt-------ttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
|||||   | |  | || |  | |||  |   ||| ||        ||  ||       ||||| ||       ||||||| || ||  | || ||||| |||||||||||||| |||||||| || |||||||||||||| |||||||| ||| | || |||||||| ||||| ||||
gtaagtggccaaatgttaagttattaccatctttcttttcattccttgatttgatctttatattattataacaattcagGAATACAATTCTAAGCTCTCAGATTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3
----gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgt-----atttgctaacatattttttt-cagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
    ||| |  |   |||| |    ||   | |  || | ||  ||||        || |   || | |  | |||  |||| || || || || || ||||||||||||||||| |||||||| |||||||| || || |||||||| || || || || |||||||||||||| ||||
gtatgtaggtgaaggtattaattatttcttattcatcctccaaccaaaaagcaaaaatctaaaaaaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 4
gtaagcaactatattgaaatgttaaaaatattcattcatacaaatgtatttg-ctaacatattttt--ttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
|||||   |   |     |   ||| | |    |||    |   | | || | |||| ||        |||||||||| || || || ||||| || ||||| ||||| |||||||| || || ||||||||||| |||||||| ||| |||| |||||||| ||||| || |
gtaagtgcccgaaact--acaataagattgcatatttcctcctttttgttagtctaatattgccccaattcagGACTACAATGCCAAGCTCTCAGACTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGGGTGATGGGAACCTATGGTTACG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4
-----gtaagc-aactatattgaaatgttaaaaatattc---attcat------acaaatgtatttgctaacatattt-ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
     || ||  ||| |     ||   ||  || ||||    || |||      ||| |   |  |   |||||| || |||| |||| || || || || ||||||||||||||||| || |||||||| ||||| || || || |||||  | || || || ||||||||||||||||| ||| 
ggtatgtgagttaaccaggaaaaaggtttttaattattttctatccatcctccaacataaaaacataaaaacataattgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagcaactatattgaaatgttaaaaatat-tcattcatacaaatgtatttgctaacatattt--ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
||| | | || |       |   |  || || | ||   | ||||| | ||  | || | ||    || ||||||||| || |||||||| || |||||||||||||| |||||||  ||||| |  |  ||||| ||||| || |||||||| ||||| |||||||| ||||
gtacgtatctcttactctttaggatcaacatcttatatttgcaaattttttaaccaataaatcccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT3G28690.1 (Arabidopsis thaliana), 3'ss of exon 3
--------gtaagcaactatattgaa--atgttaaaaatattcattc-----atacaaatgtattt---gctaacatatttt--tttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
        | |||| |||  |    |  |  | ||   | | | |||     ||    ||  ||||      || ||  |    || ||||| ||||| ||||| |||||||||||||| ||||| |||||||  || || |   | ||| | || || |||||  | ||||||||||| ||||| ||||
gtatgtctgaaagccacttaacccgataacctcaactctgtcctttctctctatgtttataaattttagaaaaaaatgctcccattgcagGAATATAATGCAAAGCTCTCTGATTTTGGGCTTGCAAAAGATGCTCCAGACGAGAAAAAATCCCACGTATCAACCCGAGTCATGGGAACTTATGGTTATG

upper sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcaacta----tattgaaatgttaaaaatattcattcatacaaatgtatttgctaac--atatttt-tttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
||||| ||  |    | |   ||  | |    | |    | |||  | |  || |  ||    | ||  | |||||||| || || || ||||| |||||||||||||||||||||||||| || ||||| ||||| || ||||| || ||  | || |||||||| ||||||||||
gtaagtaataaaaactgtgataaattcacgtttgtctcctaatatcattccatcttttatatgacatcctatttcagGAGTACAATGCCAAACTTTCTGATTTTGGACTTGCTAAAGATGGTCCCGAGGGAGATAAGACTCATGTATCTACCCGTGTTATGGGAACTTATGGATATG

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|211372816|gb|FL333609.1|FL333609
EST:     CTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: CTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|32938653|gb|CF043472.1|CF043472
EST:     GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCG                         GACCATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|32938832|gb|CF043651.1|CF043651
EST:     GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|71595774|gb|DR906525.1|DR906525
EST:     GACCAGTAATCTATCGGGACTTCAAAACCTCCGATATTCTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGTCCTGAG
genomic: GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|211273746|gb|FL307651.1|FL307651
EST:     CTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: CTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|50323063|gb|CO518189.1|CO518189
EST:     GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|211110588|gb|FL337469.1|FL337469
EST:     CTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: CTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|211053378|gb|FL364311.1|FL364311
EST:     GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: GACCAGTAATCTATCGGGACTTCAAAACCTCCAATATTCTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
EST: gi|211474780|gb|FL319638.1|FL319638
EST:     CTTTTAGATGCG                         GACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG
genomic: CTTTTAGATGCGgtaagcaact ... tttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatgttaaaaatattcattcatacaaatgtatttgctaacatatttttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG
                                   tgctaac  putative branch site (score: 1)
                                           tatttttttc  CT-rich tract
      ttaaaaatattcattc  TA-rich tract