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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagctggaattgccatgtttgcatttgaaataatttggcacactgatatgtccttgccattgctcatgagtgacctgtcaaatttgtttacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTGACCCAAAGGGATCCCAGAAGAAGGAAATGGAAGAA

Basic information

species Zea mays
transcript GRMZM2G151863_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os11g28300.1 (Oryza sativa), 3'ss of exon 5
tgtagctggaattgccatgtttgcatttgaaataatttggcacactgata-tgtccttgccattgctcatgagtgacctgtcaaatttgtttacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTGACCCAAAGGGATCCCAGAAGAAGGAAATGGAAGAA
   |  ||| |  |       ||   |  || | |   ||| |    | | |    || |||||  |      | |  | || | ||||||| ||||| |||||||||||| ||||||||||||||  || | || ||||| ||||| ||||||||||||||||| |||||||||||||||||||||
-aaatttggtaaggttgaaaatggcatcaaagtgaacaggcccttatacactaatattcccattattttctcataatttatctactttgtttccctgctagTTTTGTACTTGTTCTTTGGACTACGTTTGTTATACATTGCTTGGAAGTCTGACCCAAAGGGATCTCAGAAGAAGGAAATGGAAGAA

upper sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 5
-tgtagctggaatt--gccatgt--ttgcatttgaaataatttggcacactgatatgtccttgccattgctcatgagtgacctgtcaaatttgtttacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTGACCCAAAGGGATCCCAGAAGAAGGAAATGGAAGAA
 |||   |  || |     |||   ||  |||   | | ||||||     ||| |||   ||   || |  | |   || ||  |  | | | |||   ||  |||| | ||   ||| || ||||| |||||||| |||||||| |||| ||| ||  |||||| ||||||||| ||||||||||| |||
atgtttttccaacttgattatgcaattaaattatgagtcatttgggcttttga-atgaggttaatat-gaacttagatgtcccat--actctttttgtgtgt-agTTCTTTATGCATTTTTCGGACTGCGGCTGCTTTATATTGCTTGGAGATCAGATTCAAAGGCATCCCAGAAAAAGGAAATGGAGGAA
















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|78073958|gb|DV502392.1|DV502392
EST:     AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG                         TTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
genomic: AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAGgtacttatgt ... tacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
EST: gi|74239214|gb|DT647128.1|DT647128
EST:     AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG                         TTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
genomic: AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAGgtacttatgt ... tacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
EST: gi|88747529|gb|DY531670.1|DY531670
EST:     AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG                         TTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
genomic: AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAGgtacttatgt ... tacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
EST: gi|149055348|gb|EE156262.2|EE156262
EST:     AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG                         TTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
genomic: AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAGgtacttatgt ... tacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
EST: gi|60358343|gb|DN225316.1|DN225316
EST:     AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG                         TTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
genomic: AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAGgtacttatgt ... tacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
EST: gi|60348226|gb|DN215199.1|DN215199
EST:     AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAG                         TTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG
genomic: AATAGTGCCCAACTTGATATCAAGGAAGCACACTAATAGTGCTGCTACAGgtacttatgt ... tacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatatgtccttgccattgctcatgagtgacctgtcaaatttgtttacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTGACCCAAAGGGATCCCAGAAGAAGGAAATGGAAGAA
 cactgat  putative branch site (score: 3)
                                       tttgttt  putative PPT
                                    aaatttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagctggaattgccatgtttgcatttgaaataatttggcacactgatatgtccttgccattgctcatgagtgacctgtcaaatttgtttacctgccagTTTTGTACTTATTCTTTGGACTACGGCTGCTGTATATTGCATGGAAATCTGACCCAAAGGGATCCCAGAAGAAGGAAATGGAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA