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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacaatgacaccgccgccattattgacgcatgcaattcgtagcgcacgtgctcattctctctctctcccatggtggtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTGCTGGAGGTGATGCGGGAGCCGTACGGCGTATGGTCGTCGTCGGCGCCGC

Basic information

species Zea mays
transcript GRMZM2G139372_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139372_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g02820.1 (Oryza sativa), 3'ss of exon 7
gtacgtacaatgacaccgccgccattattgacgcatgcaattcgtagcgcacgtgctcattctctctctctcccatggtggtgc-tggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTGCTGGAGGTGATGCGGGAGCCGTAC---GGCGTATGGTCGTCGTCGGCGCCGC
||| ||||        |||||||   || | |      ||  || ||| | || ||| | |    |   ||     | |  ||| | ||||  | ||||||  |||||||| ||||||||||||||  |||||||||||||||||||||||| ||||||| |||||   ||||| ||| ||||| ||  |    
gta-gtacgccccgctcgccgccgccatggccatg---aacgcg-agctcgcgagctgactactccgagctggttggtttctgcattgcagGTGAGGGACAGCGAGGTGGCGGTGCAGGCGGACAGGGTGAGGGACTCGCTGCTGGAGGTGACGCGGGAGACGTACCCCGGCGTGTGGCCGTCGCCGCAGG---
















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|149008798|gb|EE040999.2|EE040999
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|148939035|gb|EC883422.2|EC883422
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|211381014|gb|FL454999.1|FL454999
EST:     TCAACGTCACCTCCCACGAGAGCYTCGTCCTCAACGTYTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|149094876|gb|EE180453.2|EE180453
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|149082524|gb|EE171718.2|EE171718
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTTTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|211201034|gb|FL469044.1|FL469044
EST:     TCAACGTCACYTCCCACGAGAGCCTCGTCCTMAACGTYTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|211302585|gb|FL473407.1|FL473407
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATKAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|211093504|gb|FL436332.1|FL436332
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|110958139|gb|EE178191.1|EE178191
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|211093503|gb|FL436331.1|FL436331
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|211223092|gb|FL467855.1|FL467855
EST:     TCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
EST: gi|149096500|gb|EE182245.2|EE182245
EST:     TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCC                         AGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG
genomic: TCAACGTCACCTCCCACGAGAGCCTCGTCCTCAACGTCTTCCGCGCCGCCgtacgtacaa ... gtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtacaatgacaccgccgccattattgacgcatgcaattcgtagcgcacgtgctcattctctctctctcccatggtggtgctggcagAGGCGGGACAATGAGGTGGCAGTGCAGGCGGACAGACTGAGGGACTCGCTGCTGGAGGTGATGCGGGAGCCGTACGGCGTATGGTCGTCGTCGGCGCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG