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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgggtaggaaagacttaagtgaaagaactcaaccccttgctattcatgttccttgcctgttgaatttcagttgacacacttgaaatgttctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG

Basic information

species Zea mays
transcript GRMZM2G064898_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064898_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g26940.2 (Oryza sativa), 3'ss of exon 1
-----atgggtaggaaagacttaagtgaaagaactcaaccccttgctattcatgttccttgcctgttgaatttcagttgacacacttgaaatgttctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG
      || ||  ||       || |   ||  ||||||     |||| |  |  | | | |    || |||| |||  |     ||  ||| || | ||  ||||||||||| |||||||||||||||||||| ||||| || |||||||||||||||||||||||||||| |||| | || |||||||| |||||||| || |
agggcttgagttagatgtctacaatttgtagtcctcaacattcagctactagtactacatac----tgtatttaagtaaattttattttaatttttt-ttggcagATCACTTATCACTTCTTCCATTGGAAGAAGGGAACTCCATTTGCTGCTGATGACCAAGGCATCTACAACAGACTAACTTGGTGGGAACAAATTGATAACG

upper sequence: GRMZM2G064898_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv15s0046g00140.t01 (Vitis vinifera), 3'ss of exon 1
atgggtaggaaagacttaagtgaaagaactcaaccccttgctat-tcatgtt-ccttgcctgttgaatttcagttgacacacttgaaatgttctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG---
  |  |    |     |  ||      || |  ||   |||||  | |  || | ||   |  |   | | |  |||   |   | |   |||    || || |||| || |||||||||||||||||||||||||| ||||||||||   | ||||| || |||||||  || ||||| ||||||||||| || |||||||   
--gtttgtttatcttctttgtctgtatacccttcctgatgctacattagattactttatatcctctctatgacctgattgaggagcatgcttcacactttagGTCACCTATCACTTCTTCCATTGGAAGAAAGGAACTCCTTTTGCTG---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|211356382|gb|FL426368.1|FL426368
EST:     TTGCTCCCCGGGGGCAGCCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: TTGCTCCCCGGGGGCAGCC-TGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211274084|gb|FL097598.1|FL097598
EST:     GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211274087|gb|FL097601.1|FL097601
EST:     GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211272284|gb|FL097591.1|FL097591
EST:     GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211274085|gb|FL097599.1|FL097599
EST:     GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|211274086|gb|FL097600.1|FL097600
EST:     GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
EST: gi|14243683|gb|BG841365.2|BG841365
EST:     GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCC                         ATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT
genomic: GTTGCTCCCCGGGGGCAGCCTGGACCGTCGTCAACCTCGCGCACTTCGCCgtgagtcccc ... ctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttccttgcctgttgaatttcagttgacacacttgaaatgttctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG
                        agttgac  putative branch site (score: 4)
                                           ttctattttc  putative PPT
                                      aaatgttctatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgggtaggaaagacttaagtgaaagaactcaaccccttgctattcatgttccttgcctgttgaatttcagttgacacacttgaaatgttctattttcagATCACTTACCACTTCTTCCATTGGAAGAAAGGAACCCCTTTTGCTGCTGATGACCAAGGCATCTACAGCAGATTGACATGGTGGGAGCAAATTGACAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA