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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctcaaatgaagagtgaaattagttgctttgtttacaggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT

Basic information

species Zea mays
transcript GRMZM5G871262_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G871262_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g03760.1 (Oryza sativa), 3'ss of exon 12
--------------------------gtgagtct-caaatgaagagtgaaattagttgc-tttgtttaca-ggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT---------------------------------
                          || ||| | ||  ||     |  ||| || ||  | | |  |   |||     |  |   ||  ||   |||||  |  | ||||  || |||  |  || ||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| ||||||                                 
gtatgtatctagcatgcaaatccatagtcagtttacagttgtttgctcgaataagctggatatatccatgtggtggatattggagcatcaaacttttgaaaatgttctgat--tttaacatctgaatatgcagGTACAATGTTTTCCAGTATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTTGTAAGTGCATTCTTCCAAAGTATTCAGTCAATT

upper sequence: GRMZM5G871262_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g03760.2 (Oryza sativa), 3'ss of exon 12
--------------------------gtgagtct-caaatgaagagtgaaattagttgctt-tgtttaca-ggtattgctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT
                          || ||| | ||  ||     |  ||| || ||  | | |  |   |||     |  |   ||  ||   |||||  |  | ||||  || |||  |  || ||||||||||||||||||||||||||||||||| |||||||| || ||||||||||| |||||||| ||||||
gtatgtatctagcatgcaaatccatagtcagtttacagttgtttgctcgaataagctggatatatccatgtggtggatattggagcatcaaacttttgaaaatgttctgat--tttaacatctgaatatgcagGTACAATGTTTTCCAGTATGGCTTTGTGGCTCTTGCGATACTCACACTCTTTTACTATGCAATATTT
















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|89251977|gb|DY623763.1|DY623763
EST:     ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT
genomic: ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT
EST: gi|78121981|gb|DV540365.1|DV540365
EST:     ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAA                         GTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT
genomic: ATCTTTGGCCACACATTGCAATCCCTTCGTGGAATTAAGTATCTTTACAAgtgagtctca ... aaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtggatatttaaaacttgaacgtactttgatacttgaaccacaaaacatgcagGTACAATGTTTTCCAGTATGGCTTTGTTGCTCTTGCCATCCTCACACTCTTCTACTATGCTATATTT
                          ctttgat  putative branch site (score: 5)
      atatttaaaacttgaa  TA-rich tract