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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcaaatgggtaggaggacttaagtgaaagacgtcaactccttgctattcatgttccttgccaattgaatttcagttgacacacttgaatctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG

Basic information

species Zea mays
transcript GRMZM2G044720_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044720_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
gtcaaatgggtaggaggact-taagtgaaagacgtcaactccttgctattcatgttccttgccaattgaatttcagttgacac-acttgaatctatttt--cagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG
      || ||  || | ||  || |   || | |||||     |||| |  |  | | | |    || |||| |||  |    | || ||| | ||||  ||||||||||| |||||||||||||||||||| ||||| || |||||||||||||||||||||||||||| |||| | || |||||||| |||||||| || |
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatac----tgtatttaagtaaattttattttaattttttttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG

upper sequence: GRMZM2G044720_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1
--------gtcaaatgggtaggaggacttaagtgaaagacgtcaactccttgctattcatgttccttgccaattgaatttcagttgacacacttgaatctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG---
         ||   |  ||  |   ||        | | |  ||     || || |  ||  ||  |   |  |||       ||||    | ||  ||    || || |||| || |||||||||||||||||||||||||| ||||||||||   | ||||| || |||||||  || ||||| ||||||||||| || |||||||   
gtttgtttatcttctttgtctgtatacccttcctgatg-ctacattagattactttatatcctctctatgacctga-------ttgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTG---AAGACCAGGGAATCTACAATAGGTTGACGTGGTGGGAGCAGATAGACAATGGAA
















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|211339123|gb|FL064683.1|FL064683
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211252164|gb|FL064672.1|FL064672
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|78086263|gb|DV514656.1|DV514656
EST:     GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211339126|gb|FL064686.1|FL064686
EST:     GTTGCTCCCCCGGAS-AGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|60338514|gb|DN205487.1|DN205487
EST:     GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|37380052|gb|CF626807.1|CF626807
EST:     TCGTAAACCTCGCGCACTTGGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAGGGAACCCCTTTTGCTGCTGAT
genomic: TCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211126309|gb|FL371369.1|FL371369
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211252163|gb|FL064671.1|FL064671
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211252166|gb|FL064674.1|FL064674
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211252165|gb|FL064673.1|FL064673
EST:     GTTGCTCCCCCGGAG-AGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCTACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGA
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATC-ACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGA
EST: gi|78025996|gb|DV494383.1|DV494383
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|33103669|gb|CF063629.1|CF063629
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211339125|gb|FL064685.1|FL064685
EST:     TTGCTCCCCCGGAG-AGTCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTC
genomic: TTGCTCCCCCGGAGCAG-CCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTC
EST: gi|32844760|gb|CD984441.1|CD984441
EST:     GTTGCTCCCCCGGAGCAGCCTGGACCGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|149084440|gb|EE173898.2|EE173898
EST:     GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211339127|gb|FL064687.1|FL064687
EST:     GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAMGGAACCCCTTTTGCTRCTGAT
genomic: GTTGCTCCCCCGGAGCAGCCTGGACGGTCGTAAACCTCGCGCACTTCGCCgtgagttccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcatgttccttgccaattgaatttcagttgacacacttgaatctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG
                            agttgac  putative branch site (score: 4)
                                            tctattttc  putative PPT
                 aattgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcaaatgggtaggaggacttaagtgaaagacgtcaactccttgctattcatgttccttgccaattgaatttcagttgacacacttgaatctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - tccttgc
- - - - - - - - - - - - - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgaat