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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagttgatatgataatttgaccgcaatgttgtattactctgattttttcccaagttctgttcataggttaaacctgcaattcttatatgtttttgcagGTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTGGATGCTCGAACCTTTTGCTTTGGAGTTCGAATTGTTAGGAGGAGGACTG

Basic information

species Zea mays
transcript GRMZM2G155123_T03
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155123_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g03430.3 (Oryza sativa), 3'ss of exon 6
tgtagttgatatgataatttgaccgcaatgttgtattactctgattttttcccaagttctgttcatag-gttaaacctgcaattcttatatgtt--tttgcagGTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTGGATGCTCGAACCTTTTGCTTTGGAGTTCGAATTGTTAGGAGGAGGACTG
  | ||||  |   |  |||      |||  | |||| |     ||||    |  |    | |  ||   | |  |      || || |   ||  ||||||| ||||||||||||||||||| || || || |||||| ||||||| || || |||||||| || ||||||||||| |||||||||| ||   |||||||||
gcttgttgccacattgctttacttttaat--tatatttccaaagttttggttct-gcatagcttgtactatcattctcatggttgttttccctttatttgcagATAACCACATGCAGTAGAGAGGGAATTAATAAAATTTGCTTATCAAGGGTCGATGCTCGGACATTTTGCTTTGGTGTTCGAATTGCTAAACGGAGGACTG
















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|30306927|gb|CD001600.1|CD001600
EST:     TGGGCGGGATGATGGGCCACTG                         GTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTG
genomic: TGGGCGGGATGATGGGCCACTGgtgagtttat ... gtttttgcagGTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTG
EST: gi|211212018|gb|FL385215.1|FL385215
EST:     GGCCTGGTTCTCAGTTACTAGGGATAAATGGGCGGGATGATGGGCCACTG                         GTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTG
genomic: GGCCCGGTTCTCAGTTACTAGGGATAAATGGGCGGGATGATGGGCCACTGgtgagtttat ... gtttttgcagGTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTG
EST: gi|161583099|gb|EY955120.1|EY955120
EST:     CGGTTCTCAGTTACTAGGGATAAATGGGCGGGATGATGGGCCACTG                         GTAACCACATGCAGTAGAGAAGGGATCAAACAAAATTAGCTTATCTAGAGT
genomic: CGGTTCTCAGTTACTAGGGATAAATGGGCGGGATGATGGGCCACTGgtgagtttat ... gtttttgcagGTAACCACATGCAGTAGAGAAGGGATCAA-CAAAATTAGCTTATCTAGAGT
EST: gi|166577894|gb|EG036160.1|EG036160
EST:     GGCCCGGTTCTTAGTTACTAGGGATAAATGGGCGGGATGATGGGCCACTG                         GTAACCACATGC
genomic: GGCCCGGTTCTCAGTTACTAGGGATAAATGGGCGGGATGATGGGCCACTGgtgagtttat ... gtttttgcagGTAACCACATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcccaagttctgttcataggttaaacctgcaattcttatatgtttttgcagGTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTGGATGCTCGAACCTTTTGCTTTGGAGTTCGAATTGTTAGGAGGAGGACTG
                                            tgttttt  CT-rich tract
                                  aattcttatatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtagttgatatgataatttgaccgcaatgttgtattactctgattttttcccaagttctgttcataggttaaacctgcaattcttatatgtttttgcagGTAACCACATGCAGTAGAGAAGGGATCAACAAAATTAGCTTATCTAGAGTGGATGCTCGAACCTTTTGCTTTGGAGTTCGAATTGTTAGGAGGAGGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA