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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggtctaatatgaaatagatagtatttgcattactcaattgattgattgatgcatgcagtctttgtgcttattccattgcatgtgtttttcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG

Basic information

species Zea mays
transcript GRMZM2G149224_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g29170.1 (Oryza sativa), 3'ss of exon 1
--ttggtctaatatgaaatagatagtatttgcattactcaattgattgattgatgcatgcagtctttg-tgcttattccattgcatgtgtttttcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG
  |||    | ||    ||   |   |   | || |   | |       |       | || | |||| ||   | | |||   || | || || || |||||||||||| ||||| || || |||||||| |||||||| |||||||| || ||||||||||| ||||||||||||  ||| ||||| || |
cattgactcactactttattctttagagccgaataaaatagtgtgacattactcaatttcattgtttgatgtccaatgcat---atatattcttaatgtgcagCTTTTGAGGGGGCTGATGTTGTTTTCCACATGGCTGCACCAGATTCGTCTATCAACAACTTTCACCTTCATTATTCAGTTAATGTTGAGG

upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 1
lower sequence: AT1G47290.1 (Arabidopsis thaliana), 3'ss of exon 2
ttggtctaatatgaaatagatagtatttgcattactcaattgattgattgatgcatgcagtctttgtgcttattccattgcatgtgtttttcatctg-cagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG
                      ||||||    | |  | |  ||   ||  | ||   | || | |   |  ||    |   ||    | |  |    ||| |||| |||| |||||||| || || |||||||| |||||||||||||| || |||||   ||| ||||| ||   ||| |||||  | |
----------------------gtatttttgcttcgaattcaat---ttagttcagtgattcgtcgaattcgtttttgtatctgaagatatagtgaaacagGTTTTCAAGGAGCAGAAGTGGTGTTTCATATGGCAGCTCCAGATTCATCGATTAACAATCACCAGCTTCAGTACTCAGTTAATGTTCAAG

upper sequence: GRMZM2G149224_T03 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g02200.t01 (Vitis vinifera), 3'ss of exon 2
---ttggtctaatatgaaatagatagtatttgcattactcaattgattgattgatgcatgcagtctttgtgcttattccattgcatgtgtttttcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG
    |||      |||  | |  |  ||| || |  | |  |||||    || |       | | | || | | ||    |  ||  ||||||   ||  |||| |   |||| || || |  |||||||| ||||||||||||||||||||||| |||||   ||| || ||| ||  |||||||||  | |
attgtggggcgggatgttaaaacttatatctgta--attggattgaacatttta-atccctattatatgggttgatcttgtctcacatgttttgattccacagCATGCCAAGGAGCTGAGGCTGTTTTCCACATGGCTGCTCCAGATTCATCCATTAACAATCACCAGCTCCATCATTCAGTCAATGTGCAAG

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|211074088|gb|FL056288.1|FL056288
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211071353|gb|FL056276.1|FL056276
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211074089|gb|FL056289.1|FL056289
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|149072461|gb|EE160738.2|EE160738
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211071352|gb|FL056275.1|FL056275
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211071351|gb|FL056274.1|FL056274
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATA
EST: gi|211071355|gb|FL056278.1|FL056278
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211074087|gb|FL056287.1|FL056287
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211074092|gb|FL056292.1|FL056292
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211074086|gb|FL056286.1|FL056286
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211071358|gb|FL056281.1|FL056281
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211074085|gb|FL056285.1|FL056285
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211074083|gb|FL056283.1|FL056283
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
EST: gi|211071356|gb|FL056279.1|FL056279
EST:     GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAG                         CTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA
genomic: GGCCGTCTACGTGTCCGCCGACCTCCGTGACAAGGCCCAGGTCGCCAGAGgtgcgtggtc ... tcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgatgcatgcagtctttgtgcttattccattgcatgtgtttttcatctgcagCTTTTGAAGGGGCAGAAGTAGTTTTCCATATGGCTGCTCCAGATTCATCCATCAACAACTTCCACCTTCATTATGGAGTCAATGTCGATG
 gattgat  putative branch site (score: 4)
                                         tttttcatct  putative PPT
                                         tttttcat  TA-rich tract