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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggagaatttccttttatagactgtaatatactgggttcaacttctgtcctcctactagcagcctgcaacagtcttcagtattactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT

Basic information

species Zea mays
transcript GRMZM2G020721_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g19970.1 (Oryza sativa), 3'ss of exon 6
--ggagaatttccttttatagac-tgtaatatactgggttcaacttctgtcctcctactagcagcctgcaacagtcttcagtattactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT
    |    |   |   ||| |  |||  | || |  |||   | ||| |  ||              ||   || ||||| |||  |||  || |||  |||||||| || ||||||||||| ||||||||||||||||| || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| || |
ctcaatgcctcaatagcatacatgtgtggt-tagtaagtttttcatctatgttcaagtgcatgcatatcacttgttttcagcattgatttccctcatt--cagGTGCTGTTTTTGATGTACCACTACTTCAATGCTAAAGAGATATACAATGCAATTCGTGTGTTCATTGCTGCATATGTCTGGATGACTGGATTTGGTAACT

upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA17G04070.1 (Glycine max), 3'ss of exon 6
ggagaatttccttttatagactgtaatatactgg-gttcaacttct---gtcctcctactagcagcctgcaacagtcttcagtattactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT
     || |  || |  |     |  | ||||    || ||  |      | || | | |   |   | | | |   || | || |     ||||   |  |||||  | || |||||||| ||||||||   |||    ||||||||||||||||||||| ||||||| ||||||||||| ||||||||||||||||| || |
atcagatctgattattcatctctttctgtacttacatttaatgttataaattcttcaaattttaatattccata--ttttaataatttgacatctg--taacagGTTTTGTTTTTGATGTATCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTATGGATGACTGGATTTGGGAACT

upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G36550.1 (Glycine max), 3'ss of exon 6
ggagaatttccttttatagactgtaatatactgggttcaacttctgtcctcctactagcagcctgcaacagtcttcagt---attactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT
  ||| ||||   ||||  | | |  |    |   | ||  |  |||  |        ||   |  |||| ||   | |   || | || |  |   |  |||||  | || |||||||||||||||||   |||    ||||||||||||||||||||| ||||||| ||||||||||| ||||||||||||||||| || |
--agattttctgattattca-tctcttgctgtacttacatttaatgttataaattcctcaaattttaacattccatatttttatcatttgacatccgtaacagGTTTTGTTTTTGATGTACCATTACTTTGCTGCATCTGAAATCTACAATGCAATCCGTTTGTTCATTGCTGCATATGTTTGGATGACTGGATTTGGGAACT

upper sequence: GRMZM2G020721_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0077g00620.t01 (Vitis vinifera), 3'ss of exon 6
----ggagaatttccttttatagactgtaatatactgggttcaacttctgtcctcctactagcagcctgcaacagtcttcagtattactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT
    | || |  |  |  || | ||| |  | | |  | || |  |||||   ||    |      |  |    ||||       |  ||  ||||   | |||||  |||| |||||||| ||||||||    || | ||||||||| ||||| |||||  | || || ||||||||||| ||||||||||||||||| ||||
atatgtaggaacta-tcctagacacttttgt-tgccagctttatattctgctttctagatgttcatcatcggtggtctc--actctctttcttctatcctacagGTATTATTTTTGATGTATCATTACTTTGCGGCAACAGAAATCTATAATGCCATCCGCCTTTTTATTGCTGCATATGTGTGGATGACTGGATTTGGGAATT

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|148982690|gb|EE028501.2|EE028501
EST:     TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAG                         GTGCTATTCTTGATGTACCATTACTTCAATGCTNAAGAAATCTACAATGCA
genomic: TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAGgtacttatca ... taatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCA
EST: gi|148986950|gb|EE030765.2|EE030765
EST:     TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAG                         GTGCTATTCTTGATGTACCATTACTTNCA-TGCTAAAGAAATCTACAATGC
genomic: TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAGgtacttatca ... taatttccagGTGCTATTCTTGATGTACCATTACTT-CAATGCTAAAGAAATCTACAATGC
EST: gi|71448158|gb|DR829208.1|DR829208
EST:     TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAG                         GTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCA
genomic: TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAGgtacttatca ... taatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCA
EST: gi|91875375|gb|EB405332.1|EB405332
EST:     TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAG                         GTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCA
genomic: TACTGTACTTGAATAGGCATCAAACTGAAGAATGGAAGGGTTGGATGCAGgtacttatca ... taatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctcctactagcagcctgcaacagtcttcagtattactttatctaatttccagGTGCTATTCTTGATGTACCATTACTTCAATGCTAAAGAAATCTACAATGCAATCCGTGTGTTCATCGCTGCATATGTCTGGATGACTGGATTTGGCAATT
                                          atctaat  putative branch site (score: 3)
                                      ctttatct  CT-rich tract
                                 tattactttatctaat  TA-rich tract