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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcccagctcaatacagcccattgatgtgcaggcatatcagatatatcgattgtaattgcgtttgaagttcacttattaccattcgtgatatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAGGACACTCTAAGAAAAGCAGCGCATGCGTGGAAGCGGATTGTCGAGCTAC

Basic information

species Zea mays
transcript GRMZM2G052389_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052389_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g01390.1 (Oryza sativa), 3'ss of exon 1
gtgcccagctcaatacagcccattgatgtgcaggcatat-cagatatatcgattgtaattgcgtttgaagttcacttattaccattcgtgatatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAGGACACTCTAAGAAAAGCAGCGCATGCGTGGAAGCGGATTGTCGAGCTAC
||  ||  |||  | |   | | || |     |  |||  || |   ||| |||    |  |  | |   | |    |||           |     | |||| |||||||||||||||||||| |||||| ||||||||||| ||||||||||||| || ||||| ||||| |||||||||||||| || |||||||| |
gtagcctcctctttgctaacaaatgctaaaatgctataaacaaaacaatccattacgctcacaat-ggtttccttacatttttgactcctttccaatctagGTGTTCCGCAAGGATAACAGGACTATGCTCCCCAGGAAGGAGCTGTTCAAGGACACACTCAGAAAGGCAGCCCATGCGTGGAAGCGTATCGTCGAGCTCC
















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|149085342|gb|EE174848.2|EE174848
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
EST: gi|71429539|gb|DR810589.1|DR810589
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
EST: gi|148931792|gb|EC875082.2|EC875082
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
EST: gi|71438259|gb|DR819309.1|DR819309
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
EST: gi|71435701|gb|DR816751.1|DR816751
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
EST: gi|211132739|gb|FL016687.1|FL016687
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
EST: gi|211132736|gb|FL016684.1|FL016684
EST:     ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCT                         GTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG
genomic: ACGCCGTCCACGTCGCCGACCGCATGGCGCGCCTCGTCGCATCCGACCCTgtaagccgcc ... tatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcgattgtaattgcgtttgaagttcacttattaccattcgtgatatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAGGACACTCTAAGAAAAGCAGCGCATGCGTGGAAGCGGATTGTCGAGCTAC
     attgtaatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcccagctcaatacagcccattgatgtgcaggcatatcagatatatcgattgtaattgcgtttgaagttcacttattaccattcgtgatatgtaccagGTCTTCCGCAAGGATAACAGGACCATGCTCTCCAGGAAGGAGTTGTTCAAGGACACTCTAAGAAAAGCAGCGCATGCGTGGAAGCGGATTGTCGAGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG