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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcatatgtttcttctctgctacctacttttagtgcagaactggagattatctggcatagcaatagcattgatacttcattctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 5
-------------gtgagcata-tgtttcttctctgctacctacttttagtgcagaactggagattatctggcatagcaatagcattgatacttcattct-gtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA
              | |    | | ||  ||| |  ||  |||||||||||| |  |   || |||   ||||| | |  |    |  ||| |||||||| || ||||||||||| | ||||||||||||||||| || |||| || |||||  |||| |||||| ||| ||||  ||||| |  | | |||||||   ||  |||| |
gtaagtaatgcacattattgcagtattatttcccaactgactacttttagtgtaata--agaaattcagtggcacatcc-tgaagt--ataattcattcttgtctgcagACTCACCGGAAGGCAAACAAACAGCAGAGTCCTCTGGATTTGACGTGTGTTCTTGACAAGGCCCTACAAGCTCCCGCTGTTGAAAACATACCTCACAAGA
















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|32929166|gb|CF033978.1|CF033978
EST:     ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGGATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|24934302|gb|CA452520.1|CA452520
EST:     ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|60340184|gb|DN207157.1|DN207157
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGGATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGGATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|32868675|gb|CF008357.1|CF008357
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGGATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAANNNNNNN
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAAATGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaactggagattatctggcatagcaatagcattgatacttcattctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA
                              cattgat  putative branch site (score: 4)
                                      cttcattct  CT-rich tract
        agattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcatatgtttcttctctgctacctacttttagtgcagaactggagattatctggcatagcaatagcattgatacttcattctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA