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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattcctgctgtctctgtttcaggagtagcacattcttgtacatgtattgttttctgattaccatactctaaatttggccttgcaatgttgttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG

Basic information

species Zea mays
transcript GRMZM2G107362_T04
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g11050.1 (Oryza sativa), 3'ss of exon 1
-aattcctgctgtctct-gtttcaggagtagcacattcttgtacatgtattgttttctgattaccatactctaaatttggccttgcaatgttgttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
  || | || | | |   |||  |   |  |||  |        || | ||  ||  | | ||     |||||||| ||    |||||| |  | ||  ||||||||||||||||||||||| |||||||||||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||
ctatccttgatttgtggagttctacttgatgcatgtgaaatgttatctttttcttctttactatttccctctaaatatg-ttgtgcaatttcatcttg-cagTTAGAATGCTCAGGGAAGAGCTGCAGTTGCTTCAAGAACCTGGCTCGTATGTTGGTGAGGTGGTGAAGGTCATGGGTAAATCAAAGGTTCTAGTGAAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv04s0008g04690.t01 (Vitis vinifera), 3'ss of exon 1
aattcctgctgtctctgtttca-ggagtagcacattcttgtacatgtattgttttctgattaccatactctaaatttggccttgcaa-------tgttgtttt-ttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
          ||| | ||| ||  |  |     |||||| |     |     || || | ||  | | |  |||||| |  |    |       || ||||   |||||| || |||||||| ||||| |||||| |||||||||||||||| |||||||||||||| || || || || ||||| ||||| |||||| |||| |||
---------ggtcacagttgcatagcattaggaattcttttttgctttcctattccttactagaaaaattgaaattttgattaatgaaccttggtggtgttacattcagTGAGGATGCTCAGAGAAGAATTGCAGCTGCTTCAAGAGCCTGGATCATATGTTGGTGAAGTAGTCAAAGTTATGGGAAAATCGAAGGTTTTGGTTAAG

upper sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
-----aattcctgctgtctctgtttcaggagtagcacattcttgtacatgtattgttttctgattaccatactctaaatttggccttgca-atgttgtttttt-cagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
      ||| ||| | |     ||     ||||  | | |||||       | | | |||   ||       |    || |   | |||| || || ||  |  |||| || ||||| || |||||||||||  | ||||| |||||||| |||||||||||||| || || || || |||||||| ||||||||  | || |||
gaccagattactgttctaagaattcagccagtaataaaatcttg-------agtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG

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|32848306|gb|CD987987.1|CD987987
EST:     CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|32923562|gb|CF028374.1|CF028374
EST:     CCATAACCTCAACCGGCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|211538808|gb|FL146747.1|FL146747
EST:     CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|32846583|gb|CD986264.1|CD986264
EST:     CCACAACCTCAACCGTCTCGAGGCCCAGCGCAATGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|60398970|gb|DN231786.1|DN231786
EST:     CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|211065265|gb|FL146776.1|FL146776
EST:     CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|32923495|gb|CF028307.1|CF028307
EST:     CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
EST: gi|32923161|gb|CF027973.1|CF027973
EST:     CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAG                         TTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG
genomic: CCATAACCTCAACCGCCTCGAGGCCCAGCGCAACGACCTCAACTCCCGAGgtgacatttc ... gttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgttttctgattaccatactctaaatttggccttgcaatgttgttttttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG
                     ctctaaa  putative branch site (score: 3)
                                           ttgttttttc  putative PPT
                      tctaaattt  TA-rich tract