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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcttctatttctactatttgtattgtatattatttatttgtattaatagttgatgtagttcaagtggacgtcagaaggctaacatagctgtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTG

Basic information

species Zea mays
transcript GRMZM2G147671_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 6
atcttctatttctacta-tttgtattgtatatt-atttatttgtattaatagttgatgtagttcaagtggacgtcagaaggctaacatagctgtg-----accacagGATGATGACGAT------CTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTG
   ||  ||||| | || | || ||   ||||| |||||| ||  || | |    |||  ||| |  |||||   ||  |||||| |||| ||||     | ||||||| ||||| |||      |||||||| ||||| |||||||||||||||||||  ||| |||||||  |||||||   | ||||  | ||||||||||| ||||
---tttcatttcaattagtatgcatcagatattgatttatctgagttgaga----atgctgtttagatggacaagagttggctaatatagatgtgatgtgatcacagGAAGATGATGATGCTCAGCTACTACAACAGGCTCTTGCAATGTCAATGGAGGAGGGTTCTTCAGGGGCTGCAGC---GGCTGATGCTGCTATGGCAGAGGCTG

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 6
atcttctatttctactatttgtattgtatattatttatttgtattaatagttgatgt-agttca-agtggacg-tcagaaggctaacatagctgtgaccacagGATGATGACGAT---CTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTG---
   ||   |||  |  | || | |||| |    || |||  |   |  | |   | | ||  || |||    | || |    || |  |       |   ||||| |||||  ||   || ||||||||||| ||||||||||||||||| |      |         || ||   |||  ||  | | |||| | ||||| |   
---ttgcttttggataagttctcttgttttaatttcattcttcccataaatcagtatcaggacatagtatttgatctgtgaactgattttcaaacaaaagcagGACGATGAGAATGCTCTTCTACAGCAGGCCCTTGCAATGTCAATGGATGATCCCACAATTAACCATGAAG---TGAGAGATACAGATATGTCTGAAGCAGCTG

upper sequence: GRMZM2G147671_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G08290.1 (Glycine max), 3'ss of exon 6
atcttctatttctactatttgtattgtat--attatttatttgtat--taatagttgatgtagttcaagtggacgtcagaaggctaacatagctgtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTG---
 |  |  |    || ||  ||| | |  |  |  ||| |   | |   |   | || |  ||||     ||    |   |  |       |   |  ||   | |||||  | |  |||||||||||||||||||||||||||||||| |    |||     |   ||    ||| |  ||  | | |||| | |||||     
-ttgtgaaggcatattagatgtctaggcttgaaaattcacaaggaagatgggacttaacatagtattgttgttttttgtattgaccttcaaatggaaacagGATGATGAGAATGCCCTACTACAGCAGGCACTTGCAATGTCAATGGATGATTCTGCAATTAGCCATGA---TGTAAAAGATACAGATATGTCTGAAGCATCTG

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|9254597|gb|BE345080.1|BE345080
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCG
EST: gi|33094256|gb|CF054250.1|CF054250
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCA
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCA
EST: gi|32849896|gb|CD989577.1|CD989577
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTG
EST: gi|32942828|gb|CF047647.1|CF047647
EST:     CAGAACTTGCCTCANATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAG
EST: gi|32849329|gb|CD989010.1|CD989010
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATG
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATG
EST: gi|18964426|gb|BM660999.1|BM660999
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGT
EST: gi|18659918|gb|BM500591.1|BM500591
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGANAAGCAAGAACAGCCAAAG                         GNTGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGGAGGGC
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGG-AGGGC
EST: gi|9952492|gb|BE639075.1|BE639075
EST:     CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAG                         GATGATGACGATCTACTACAGCAGGCACTT
genomic: CAGAACTTGCCTCAAATGCTGCTGCTGGTGACAAGCAAGAACAGCCAAAGgtattttcag ... gtgaccacagGATGATGACGATCTACTACAGCAGGCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagttgatgtagttcaagtggacgtcagaaggctaacatagctgtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTG
                                ggctaac  putative branch site (score: 2)
                                   taacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcttctatttctactatttgtattgtatattatttatttgtattaatagttgatgtagttcaagtggacgtcagaaggctaacatagctgtgaccacagGATGATGACGATCTACTACAGCAGGCACTTGCAATGTCAATGGAGGGCGGTGCTTCAGGATCTGCAGCTGTGACTGACTCCGCTATGGCAGAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - -tgtattg
- - - - - - - - - - - - - - - - - - - - - - - - - -tgatgta