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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacatgtttgctacggttatgtttttgcaacttgtgaatttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT

Basic information

species Zea mays
transcript GRMZM2G174919_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g07490.1 (Oryza sativa), 3'ss of exon 2
taacatgtttgcta-cggtta----tgtttttgcaacttgtgaatttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
|  || |||| ||| | | |     |||||||  | || || |       ||| ||  | | ||    | ||  |  ||   | |    |      |  |||||| ||||| ||||| ||||| || || |||||||| |||||||| ||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| |||
tgccaagtttcctagcagctgcaagtgttttttaatctggtaacacgtggtaagatagtttcgac---tactcataagctcttaaacatttggtgct--ttgcagATTGGTTATTGATAAAGAAACAGGGAAGCCAAAGGGTTATGGGTTTTGTGAGTACAAGGATGAGGAGACTGCTCTAAGTGCACGCCGGAACCTTCAAGGT

upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G36350.1 (Glycine max), 3'ss of exon 2
taacatgtttgctacggttatgtttttgcaacttgtgaat-ttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
| | || ||| ||    ||   |        ||| ||  | ||||  |||    ||||  | |      ||   | | |  |  || |   ||     |||  | || ||||||| ||| ||||| || |||||||||||||| || || ||||| ||||| || || || ||| ||||||| || || || |||||||||
tgagattttttctgtaatttcttggaactgccttttgcttcttgaccaaaggtttatttggttgaagacttgaactattcccatcttctt-ttatccacagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTATAAGGATGAAGAGACGGCTTTAAGTGCTCGACGAAATCTTCAGGGT

upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G31220.2 (Glycine max), 3'ss of exon 2
taacatgtttgctacggttatgtttttgcaacttgtgaat-ttgattaaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
| | || ||| ||    ||   |        ||| ||  | ||||  ||     ||||  | |      ||     | |  |  || |   ||   |||||  | || ||||||| ||| ||||| || |||||||||||||| || || ||||||||||| || || || ||| | ||||| || || || |||||||||
tgagattttttctgtaatttcatggaactcccttttgcttcttgaccaatggtttatttggttgaagacttgaattattcccatcttctt-ttatctgcagACTAGTTATTGACAGAGAAACTGGGAAACCAAAAGGTTATGGATTCTGTGAGTACAAGGATGAAGAGACGGCTTTGAGTGCTCGACGAAATCTTCAGGGT

upper sequence: GRMZM2G174919_T03 (Zea mays), 3'ss of exon 1
lower sequence: PP1S36_103V6.1 (Physcomitrella patens), 3'ss of exon 2
taacatgtttgctacggttatgtttttgcaacttgtgaatttgattaaaatgctattgagctatgctttttggcaactgactgctacaaat-tgcttg-----cagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
   | | | |  |||    ||| ||||  | | |   |   ||  ||  ||    || | | ||  |||| |    || |||| |  |||| |  |||     |||||||||  | || | |||||||||||| || ||||| ||||| || ||||||| ||  ||||||||||||||||| ||||| || ||||| ||||| |||
cgtcttatgtattac----atgctttttaatcatcacacaatggatagtatcagctttaccaatttttttcgtt--ctcactgatttaaatgtatttgaatcccagGTTGGTACTGGATAGAGAGACTGGCAAACCCAAAGGGTATGGATTCTGCGAGTTCAGAGACGAGGAAACTGCTCTGAGTGCTCGTCGGAATCTTCAAGGT

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|37383200|gb|CF628591.1|CF628591
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
EST: gi|71596191|gb|DR906942.1|DR906942
EST:     GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAG                         GTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA
genomic: GAGCAGCTCGTGCAGATTTGCGAAGAGGTTGGCCCAGTCGTATCCTTCAGgtgcgcttct ... ttgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaatgctattgagctatgctttttggcaactgactgctacaaattgcttgcagGTTGGTGATTGACAAAGAGACTGGCAAGCCAAAAGGTTATGGCTTTTGCGAGTACAAGGACGAGGAAACTGCTCTAAGTGCACGGCGGAACCTTCAGGGT
                             aactgac  putative branch site (score: 2)
                                       tacaaatt  TA-rich tract