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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcccttttccagtctattgattgtaattacaatgtaatttttgtcccctgtaagatatgttacagtaacattttagctaatcccaatttgcttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGCAATATTGGAGGGAGAGAGAATCTGGCATGAGCTCTCTAGCTTACTTTCT

Basic information

species Zea mays
transcript GRMZM2G430675_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G430675_T03 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os10g30610.1 (Oryza sativa), 3'ss of exon 10
-tcccttttccagtctattgattgtaattacaatg-taatttttgtcccctgtaagatatgttacagtaacattttagctaatcccaatttgcttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGCAATATTGGAGGGAGAGAGAATCTGGCATGAGCTCTCTAGCTTACTTTCT
  | |   ||   | |||   || | | | ||||| ||     ||| ||||  || | | |  |||| ||||||||||||||    | | |  ||  |||||| ||| |||||||||||||  || |||||||||||||||| |||| |||||||||||||||||| |||||||||||||||||| |||||||||| |||||
cacacaggtcacttatatcacttcttaatgcaatgatacacaatgttccct--aaaaaaagacacagcaacattttagctaactttactgtattttgtgcagCGCTGTTATGCCAGCTTGCAGCACTGCGGTCATTTTCACCAGAAAGATTGCAATATTGGAGGGAAAGAGAATCTGGCATGAGCACTCTAGCTTATTTTCT
















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|32923118|gb|CF027930.1|CF027930
EST:     AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGCTT                         CACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
genomic: AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTTgtaagtcagc ... cttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
EST: gi|32921859|gb|CF026671.1|CF026671
EST:     AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTT                         CACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
genomic: AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTTgtaagtcagc ... cttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
EST: gi|32920474|gb|CF025286.1|CF025286
EST:     AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTT                         CACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
genomic: AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTTgtaagtcagc ... cttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
EST: gi|32922314|gb|CF027126.1|CF027126
EST:     AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTT                         CACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC
genomic: AGATGATTCATTCGGTGTAGCTTCTTATGGATATACCATAATGGCAGTTTgtaagtcagc ... cttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccctgtaagatatgttacagtaacattttagctaatcccaatttgcttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGCAATATTGGAGGGAGAGAGAATCTGGCATGAGCTCTCTAGCTTACTTTCT
                                         tttgctt  CT-rich tract
                    taacatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcccttttccagtctattgattgtaattacaatgtaatttttgtcccctgtaagatatgttacagtaacattttagctaatcccaatttgcttattgcagCACTGCTATGCCAGCTTGCGTCATTGCGGTCATTTTCACCTGAAAAATTGCAATATTGGAGGGAGAGAGAATCTGGCATGAGCTCTCTAGCTTACTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG