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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcaggaagcatccattgcatgtgtttctttttttatattttaaagatagtttgcacaagaagttttcttatgtaattattttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG

Basic information

species Zea mays
transcript GRMZM2G046098_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g64780.4 (Oryza sativa), 3'ss of exon 3
gtcaggaagcatccat---tgcatgtgtttctttt---tttatattttaa--agatagtttgcacaa--gaagttttcttatgtaattattttgtt-gttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG
    | |  | |||||      || | ||  |      || | | | | |  ||  |  ||| ||||  ||| ||  || ||  ||| || ||||| |  ||||||||| || |||||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||||||||| || || ||||||
----gtatacttccatacacaaatatattcatgacacattgacactatcatcagccacattggacaaatgaacttacctcataaaatcatcttgtttggcagATCAAAACACAACAGCTTTTAAAGAAGTTGCGATAATTCGTCATCCACGTATTGGTGAATATGCATTTGGATTTATAACATCAACTGTTGTTCTTCAG

upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA04G39490.1 (Glycine max), 3'ss of exon 4
gtcaggaagcatccattg-catgtgtttctttttttatattttaaagatagtttgcacaagaagttttcttatgtaattattttgttg-----------ttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG
 ||||  ||      |||  |  || |   ||    || ||| ||| || | |  || | || ||   | | ||| || ||||| ||            | |||||||||||| || || || ||||| || ||||| || ||||| || ||  ||||||||||||||||||| || || |||||||| ||  | || |||
-tcagtgagttattgttgatacttgatagattgacgat-tttcaaatattggtacca-aggatgtaaccatttgtcatgatttttttacaatctccttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCATTTGGCTTTATTACATCAACTGTTATTCTACAG

upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G15360.2 (Glycine max), 3'ss of exon 4
-gtcaggaagcatc--cattgcatgtgttt-ctttttttatattttaaagata-----gtttgcacaagaagttttcttatgtaattattttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG
 || ||  |   |    |||  ||   ||  |  |||| | || ||   || |     ||   ||   |   |  | || | |    ||||| || | |||||||||||| || || || ||||| || ||||| || ||||| || ||  ||||||||||||| |||||||| || |||||||| ||    || |||
agtgagttattgttgatatttgatagattgacaattttcaaatattggtgacaaggatgtaaccatttgtcatgattttttttttaaattttcttttcagATCAAAATACCACTGCCTTTAAAGAGGTAGCAATTATCCGTCACCCGCGTGTTGGTGAATATGCGTTTGGATTTATTACATCAACTGTTACTCTACAG

upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT1G43130.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------gtcaggaagcatccattgcatgt-gtttctttttttatattttaaagatagtttgcacaagaagttttcttatgtaattattttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG
               |    ||| | || ||  |||| | |   || |||   ||||     |  |||| |   ||||     ||     ||  ||||||| | ||| ||||| || || || || ||||| || ||||| || ||||| || || ||||||||||| ||||||||||| || |||||| |||||   ||||||
acacaatgatttgaattcacaagtaacctttttatgttgctatgttgtttgcctttttcgtgtcctttgtaatggaagaacctttg----at--ttttgttctcagACCAAAACACTACTGCCTTTAAAGAGGTAGCAATCATCCGTCACCCTCGTATTGGTGAATACGCATTTGGATTTATTACATCATCGGTGACACTTCAG

upper sequence: GRMZM2G046098_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0031g02010.t01 (Vitis vinifera), 3'ss of exon 4
gtcaggaagcatccattgcatgtgtttctttttttatattttaaagatag----tttgcacaagaagttt-----tcttatgtaattattttgttgtt---agATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG
   || |    |    | ||||||||| | | | |   ||  || | |||    | |  | ||  ||  |     | ||| || | | |  | || ||   ||| |||||||| || ||||| ||||| || || || || |||||||||||  ||||||||||||||||||| || || |||||||| ||  ||||||||
---agcataattgtgctccatgtgtttatatatgtggtttacaatgttagcaagtgtttataattagcctaaaacttttaagtcactttcgtattctttgcagACCAAAATACCACTGCTTTTAAAGAGGTAGCTATCATCCGTCATCCACGTGTTGGTGAATATGCATTTGGTTTTATTACATCAACAGTAATCCTTCAG

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|51871157|gb|CV126041.1|CV126041
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|211391866|gb|FL013594.1|FL013594
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAGAATACGACAGCTTTTCAAAGAAAGCTGCA-TAATTCGTCATCCACG
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTT-CAAAGAA-GTTGCAATAATTCGTCATCCACG
EST: gi|50323815|gb|CO518941.1|CO518941
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|88755429|gb|DY539570.1|DY539570
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTT
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTT
EST: gi|91053372|gb|EB163790.1|EB163790
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|28910665|gb|CB331552.1|CB331552
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGAC
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGAC
EST: gi|76293651|gb|DV033219.1|DV033219
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|40287192|gb|CK327584.1|CK327584
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|74239462|gb|DT647376.1|DT647376
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
EST: gi|148949550|gb|EC895017.2|EC895017
EST:     AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAG                         ATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA
genomic: AAGGCATATATATTCAGCGTCAAAGCAAGTCAGCACTGCAATTTCACCAGgtcaggaagc ... ttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaaagatagtttgcacaagaagttttcttatgtaattattttgttgttagATCAAAATACGACAGCTTTCAAAGAAGTTGCAATAATTCGTCATCCACGAATTGGTGAATATGCATTTGGATTCATAACATCAACGGTGGTCCTTCAG
                                        ttatttt  CT-rich tract
                           ttttcttatgtaatta  TA-rich tract