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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggcgtgttgcttaatgacataacgcatggtttgtggccttacatttctgttatccatttgtcagtcagcattttaactgatgcaatcatatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA

Basic information

species Zea mays
transcript GRMZM2G108919_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 3
----taggcgtgttgcttaatgacata-acgcatggtt-tgtggccttacatttctgttatccatttgtcagtcagcattttaactgatgcaa-tcatatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA
    ||    | || |       ||   ||   || || | |   || |||| |   ||    | || ||| |||    | | | |||| ||| |||| ||| ||||||||||||||| || |||||||||||||||||||||||||| ||||| ||||| || ||||| || ||||| ||||| |||||||||||||| |||||||
tttttaattctattaccagtctgcaagcacatctgattatctaatctgacatgtacatt---tagttttcattca----tcttagtgatacaaatcatttaccgcagGTTGATTATGCATGTACCCCAGAAGAAGTGCAGCAGCATTTTCAAGCGTGTGGCACAGTCAATAGAGTGACGATCTTAACTGACAAGTTTGGACAGCCAA

upper sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
lower sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
taggcgtgttgcttaatgacataacgca-tggtttgtggccttacat-ttctgttatccatttgtcagtcagcattttaactgatgcaatcatatac----tgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA
     ||       | |    | | |||   ||||  || | | | |  | ||| |   | || | ||  | || ||   ||||    ||  | |       ||||||||||||||| ||||| ||||||||||| || |||||||| ||  | ||||| || || ||  | || ||||| |||||||||||||||||    || |
-----gtacacgcaactatgtttatgcagcagtttaaggtcctgcgtactttgtgaaggaatt-ttagcgaacacttagtctgagtttattgtttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA

upper sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
lower sequence: PP1S433_16V6.2 (Physcomitrella patens), 3'ss of exon 3
----taggcgtgttgcttaatgacata-acgcatggtttgtggccttacatttctgttatccatttgtcagtcagcattttaactgatgcaatcatatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA
    | |   ||||||   |   | |  |   |||  |||| |  |    ||   | |   |||  ||  | |    |  |   | || |  |  | |  | |||||||||||| | ||||| || ||||| ||||| || || |||||  | ||||| || || ||| | || ||||| ||||| ||||||||||||||||| |
tagttggatatgttgcaggagctcctgcatttatgagttgtagaatag--ttaacgatgatcatcagtgtgacgttgtcct--tttattctcttttctttt-cagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA

upper sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
lower sequence: EFJ15603 (Selaginella moellendorffii), 3'ss of exon 3
-taggcgtgttgcttaatgacataacgcatggtttg---tggccttacatttctgttatccatttgtcagtcagcattttaactgatgca---atcatatactgc---------agGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA
 || |  | | ||    | || |   || |  || |   |   ||||  || ||||| ||| || |  |   |  |    |    |   |   ||||  |  |||         |||| |||||  | ||||| || |||||||| ||||||||||||||| ||||||||||||| ||| ||||||| ||  | || ||||||||||| || || |
gtaagtctctcgccct-tcacgttgagcttctttcgatctttacttatcttcctgtt-tcctttggaaaaaaaaaaagagagagaaaaaatatatcagtttttgcttgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA

upper sequence: GRMZM2G108919_T06 (Zea mays), 3'ss of exon 1
lower sequence: EFJ38832 (Selaginella moellendorffii), 3'ss of exon 3
-taggcgtgttgcttaatgacataacgcatggtttg---tggccttacatttctgttatccatttgtcagtcagcattttaactgatgcaatcatatactg-----cagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA
 || |  | | ||    | || |   |  |  || |   |   ||||  || |||||  |  |     |   ||      ||   ||   | | |    ||     ||||| |||||  | ||||| || |||||||| ||||||||||||||| ||||||||||||| ||| ||||||| ||  | || ||||||||||| || || |
gtaagtctctcgccct-tcacgttgagtttctttcgatctttacttatcttcctgtttcctttggaaaaaaaagagagaaaaaatatatcagctttgcttgttactcagGTGGATTACTCGTGCACTCCCGAAGAAGTCCAGCAGCATTTCCAATCTTGTGGAACTGTGAACCGGGTGACGATTCTCACAGACAAGTTTGGACAACCGA

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|78085156|gb|DV513549.1|DV513549
EST:     AGTGGTGCATAAGTATGACAT                         GTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT
genomic: AGTGGTGCATAAGTATGACATgtaagtgtaa ... tatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgttatccatttgtcagtcagcattttaactgatgcaatcatatactgcagGTTGATTATGCTTGCACCCCAGAAGAAGTGCAGCAGCATTTCCAAGCTTGTGGAACTGTCAACAGGGTGACAATCTTGACTGACAAGTTTGGGCAGCCAA
                          attttaact  TA-rich tract