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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgacactagagaaattgtgtatacaaattcaacatatatcaatatggcaattggagaagctattcatgttgactgtagtgggtactacttgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG

Basic information

species Zea mays
transcript GRMZM2G088140_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 3'ss of exon 10
-------ttga-cactagagaaattgtgtatacaaattcaacatat---atcaatatggcaattggagaagctattcatgttgactgtagtgggtactacttgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG
       || | ||  |   |   | || |||||||    |  | |    |   | |||||| |||||||  || || |||||||| |           |   || ||||||||||||  |||||||||| ||| |||||||| || ||||| ||||||||||| || ||||||||||| ||||| |||
atggcacttaatcatcaacaatcctatggatacaaacatgaagttttcagtttttctggcaaatggagaaattagtcgtgttgactct-----------cccatgattcagGATGAACGGGAACTCAAAAGGCAGAGAAGAAAACAATCCAACAGGGAGTCTGCTCGCAGATCTAGGTTGCGTAAGCAG

upper sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT1G32150.1 (Arabidopsis thaliana), 3'ss of exon 10
ttgacactagagaaattgtgtatacaaattcaacatatatcaatatggcaattggagaagctattcatgttgactgtagtgggtactacttgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG
                 ||   ||     | | | ||  ||    |  |  ||    ||||      | |||| |||  || | | |          ||||||||    ||  | ||    || ||| | ||||| ||||||||||| ||||| |||||||| ||||| |||||||||
-----------------gtaagtatctcctaatcttacttctcctttacgtttatccaagcagcgtgt-ttgattgttttgtgaaat----------cagGATGAGAGAGAGATTAAGCGACAGAGACGGAAGCAATCCAATAGGGAATCTGCTCGTAGATCCAGGTTGCGTAAACAG

upper sequence: GRMZM2G088140_T01 (Zea mays), 3'ss of exon 9
lower sequence: AT2G35530.1 (Arabidopsis thaliana), 3'ss of exon 10
ttgacactagagaaattgtgtatacaaattcaacatatatcaatatggcaattggagaagctattcatgttgactgtagtgggtactacttgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG
                ||||   ||   |   |   | ||  | || ||  ||        ||| |      |||    |  ||    ||||   || |||| ||    ||||| ||    || ||| | ||||||||||||||||||||||| || ||||| ||||| |||||||||
---------------gtgtgcccacctttcttaggcagatttaaatcgccttt--------tatcctca--aactcagatttgtttgtcttgcaatt-agGACGATAGAGAACTTAAGCGACAGAGACGGAAGCAGTCCAATAGGGAGTCTGCTCGAAGATCAAGGTTGCGTAAACAG

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|60358086|gb|DN225059.1|DN225059
EST:     CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAG                         GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
genomic: CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAGgtttgtcttc ... tgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
EST: gi|60350100|gb|DN217073.1|DN217073
EST:     CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAG                         GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
genomic: CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAGgtttgtcttc ... tgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
EST: gi|60353486|gb|DN220459.1|DN220459
EST:     CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAG                         GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
genomic: CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAGgtttgtcttc ... tgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
EST: gi|211496290|gb|FL041702.1|FL041702
EST:     AACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAG                         GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
genomic: AACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAGgtttgtcttc ... tgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
EST: gi|71772544|gb|DR970475.1|DR970475
EST:     CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAG                         GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
genomic: CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAGgtttgtcttc ... tgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
EST: gi|32847056|gb|CD986737.1|CD986737
EST:     CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAG                         GATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT
genomic: CGTCAACAACAGTTCCAGGGGCTGTGGTCCCAGCAGAGCAGTGGACACAGgtttgtcttc ... tgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaattggagaagctattcatgttgactgtagtgggtactacttgtggttcagGATGAACATGAACTCAAAAAGCAAAGAAGAAAGCAGTCCAATAGGGAGTCTGCACGTAGATCTAGGTTACGTAAACAG
                      tgttgac  putative branch site (score: 3)
                tattcat  TA-rich tract