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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctgcactggcttcaatgaacattgttttattttcagaattgacagtattttaatctgacatatgttgttgccttttggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATACAATGGAACTAGTCAAACAGTGGCAGGGAAAACAAGTCAGAGATTCTAC

Basic information

species Zea mays
transcript GRMZM2G046816_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g06420.1 (Oryza sativa), 3'ss of exon 4
gtactgctgcactggcttcaatgaacattgttttattttcagaattgacagtattttaatctgacatatgttgttgcc---------------ttttggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATACAATGGAACTAGTCAAACAGTGGCAGGGAAAACAAGTCAGAGATTCTAC
        | | |  |   ||  |||       |  |||||||| | ||   |||||||||| | |  | ||| |||                ||||| | |  |||||||| |||||||||||||| ||||||||||| ||||| ||  | || ||||||| ||||||| |  ||  | ||||||||||||| |  ||||||| |
--------gtattaacccgaagaaactacaaccttatttcagaacttaccccattttaatctaaaaattattgctgctgctaatatgtctccattttgaattgtagGTCAAACTTCCTTGGCACAAAGTTTGTAATATATGATACCCACACTCCGTACAATGCAACTAGTGATTCACAGTCAGGGAAAACAAGCCGAAGATTCTCC

upper sequence: GRMZM2G046816_T04 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0072g00630.t01 (Vitis vinifera), 3'ss of exon 3
----gtactgctgcactggcttcaa---tgaacattgttttattttcagaattgacagtattttaatct-gacatatgtt-gttgccttttggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATACAATGGAACTAGTCAAACAGTGGCAGGGAAAACAAGTCAGAGATTCTAC
      |   |     | | || ||   |  |   |  ||| | |||| || | ||  | | |   |||  | || |||| ||   |        |||||||||||||||||||||||||| ||  |||| || ||||| || || |||||||||||  ||   |   |     | ||   ||| || | ||| ||||||
tatttcaggtcaatttttgttttaagcctataatctagtttgtgttcataaattactctctatctgtctcaaaatttgtttgtcctcccccttgtttcagGTCAAATTTCCTTGGCACAAAGTTCATAATTTATGATACACAGCCACCATACAATGGTTCTCAACTCTCCCCACCTGGCCGAACGAGCCGGAGGTTCTAC
















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|76923650|gb|DV169591.1|DV169591
EST:     GGTGATACATCTAGGTGTACAAGTAACAACACATACATTGGGAAATTAAG                         GTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATA
genomic: GGTGATACATCTAGGTGTACAAGTAACAACACATACATTGGGAAATTAAGgtactgctgc ... tggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATA
EST: gi|31355846|gb|CD440203.1|CD440203
EST:     GGTGATACATCTAGGTGTACAAGTAACAACACATACATTGGGAAATTAAG                         GTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATA
genomic: GGTGATACATCTAGGTGTACAAGTAACAACACATACATTGGGAAATTAAGgtactgctgc ... tggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATA
EST: gi|67042292|gb|CO468547.1|CO468547
EST:     GGTGATACATCTAGGTGTACAAGTAACAACACATACATTGGGAAATTAAG                         GTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATA
genomic: GGTGATACATCTAGGTGTACAAGTAACAACACATACATTGGGAAATTAAGgtactgctgc ... tggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagaattgacagtattttaatctgacatatgttgttgccttttggacttcagGTCAAATTTCCTTGGCACAAAATTTGTAATATACGATACTCATCCGCCATACAATGGAACTAGTCAAACAGTGGCAGGGAAAACAAGTCAGAGATTCTAC
                      atctgac  putative branch site (score: 3)
                                     ttgcctttt  putative PPT
             agtattttaat  TA-rich tract