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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttctggatgtgttttaacatttttatgatgcaaccttttatttgttctcatatataacatcgccatgtctgacatgctgcgtcttacttcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTGCAGTCCATGGAAGAGCAGGCTAAACTGCGCGACG

Basic information

species Zea mays
transcript GRMZM2G146020_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G146020_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os12g06520.1 (Oryza sativa), 3'ss of exon 2
ttttctggatgtgttttaacatttttatgatgcaaccttttatttgttctcatatataacatcgccatgtctgacatgctgcgtcttacttcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTGCAGTCCATGGAAGAGCAGGCTAAACTGCGCGACG
| ||| | | |||| | || | | | | | || | | | ||||| | ||| | |||| ||||||||||||||||| ||||| ||||||| || ||||| ||||||||||| ||| ||||||||||||||||||| |||||||| || || |
aatcctgtaagccaacagtttcttttgttctgtttgtgtatgtgatgtgtgccatctggtagtctcgaatctgattttttgcaattcacttgaaacccagAGGGATACATCTGGTTTAACTGCCGAGAATAGAGAGCTCAAGCTACGGTTGCAGTCCATGGAAGAGCAAGCTAAACTACGTGATG
















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|148949518|gb|EC894982.2|EC894982
EST:     TCTGCAGGCGGAGGCCACTAGGCTGTCAAGCACAGCTCACCCTGCTCCAG                         AGGGGATACAACTGGTCTAATTGCTGAAAATAGGGAGCTCAAGCTTCGGCT
genomic: TCTGCAGACGGAGGCCACTACGCTGTC-AGCACAGCTCACCCTGCTCCAGgtatggggtt ... tcaaacccagA-GGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCT
EST: gi|71445716|gb|DR826766.1|DR826766
EST:     CTCTGCAGACGGAGGCCACTACGCTGTCAGCACAGCTCACCCTGCTCCAG                         AGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTG
genomic: CTCTGCAGACGGAGGCCACTACGCTGTCAGCACAGCTCACCCTGCTCCAGgtatggggtt ... tcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTG
EST: gi|60399461|gb|DN232273.1|DN232273
EST:     CGGAGGCCACTACGCTGTCAGCACAGCTCACCCTGCTCCAG                         AGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTG
genomic: CGGAGGCCACTACGCTGTCAGCACAGCTCACCCTGCTCCAGgtatggggtt ... tcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTG
EST: gi|149102162|gb|EE188103.2|EE188103
EST:     GCACAGCTCACCCTGCTCCAG                         AGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTG
genomic: GCACAGCTCACCCTGCTCCAGgtatggggtt ... tcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttctcatatataacatcgccatgtctgacatgctgcgtcttacttcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTGCAGTCCATGGAAGAGCAGGCTAAACTGCGCGACG
                                     gtcttac  putative branch site (score: 3)
 tcttacttc  CT-rich tract
 atatataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttctggatgtgttttaacatttttatgatgcaaccttttatttgttctcatatataacatcgccatgtctgacatgctgcgtcttacttcaaacccagAGGGATACAACTGGTCTAACTGCTGAAAATAGGGAGCTCAAGCTTCGGCTGCAGTCCATGGAAGAGCAGGCTAAACTGCGCGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - ctggatg
- - - - - - - - - - - - - -tgatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgctgc