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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaactttggggtgtcaattgtcaacatcagaaaagcatacttttgtcttagcacaattgttttgtttgaactttgttatattctaatacgaacaatatcgccagtgcctatgaatgttaattattcttctgaattcacgctcttttgcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTACCCTCAAATCTGGAGATGTTGTTTCTGTTAGTGGGATGGGAAGGTTAAAG

Basic information

species Zea mays
transcript GRMZM2G105425_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G105425_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g54390.1 (Oryza sativa), 3'ss of exon 8
gtatgaactttggggtgtcaattgtc--aacatcagaaaagcatacttttgtcttagca-caattgttttgtttgaactttgttatattctaatacgaacaatatcgccagtgc-ctatgaatgttaattattcttc-----------------tgaattca---cgctcttttgcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTACCCTCAAATCTGGAGATGTTGTTTCTGTTAGTGGGATGGGAAGGTTAAAG
||| ||  | || | | || ||  ||  |   |||  ||| |||   ||| ||||| || || | ||||  | ||   | | ||   |||||    | |   |  |  |   ||  |||     |||||||    ||                 || || ||   | |||||||| |||  |||| |||| ||||| |||||||||||| |||||    | ||||||||||| || |||||  |||| |||||||||||||| ||||||||||| || ||||||
gtaagatttgtgagctatccatcttcttaggttcattaaaacatctctttatcttaacatcagtggtttactgtgggttatcttcccttctaccttggatggtgccatccacgcattattttgtttaattaccgctcataaagcaattgatatatgtatccaaatctctcttttgtttgtccagTGCTGGGGATGTCCGTGTGAATTGGTCACCAGTTTCGAAAAATGGAGTGACTCTCAAGGCTGGGGATGTTGTTTCTGTCAGTGGGATGGGGAGATTAAAG
















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|88752841|gb|DY536982.1|DY536982
EST:     GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAG                         TTCTGGTGATGTTCGTGTGAATTGGACACCACCAACAAAAAATGGAGTTAC
genomic: GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAGgtatgaactt ... gcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
EST: gi|60355226|gb|DN222199.1|DN222199
EST:     GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAG                         TTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
genomic: GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAGgtatgaactt ... gcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
EST: gi|60398114|gb|DN230930.1|DN230930
EST:     GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAG                         TTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
genomic: GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAGgtatgaactt ... gcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
EST: gi|29577131|gb|CB617243.1|CB617243
EST:     GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAG                         TTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
genomic: GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAGgtatgaactt ... gcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
EST: gi|78090612|gb|DV518986.1|DV518986
EST:     GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAG                         TTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
genomic: GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAGgtatgaactt ... gcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTAC
EST: gi|76292416|gb|DV031984.1|DV031984
EST:     GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAG                         TTCTGGTGATGTTCGTGTGAATTGGACACCCACA-CAAAAAAT
genomic: GCCAGTGCAGGATTTAAAATCTCACGCACGAAGCTTGCTAGCTTGATAAGgtatgaactt ... gcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgcctatgaatgttaattattcttctgaattcacgctcttttgcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTACCCTCAAATCTGGAGATGTTGTTTCTGTTAGTGGGATGGGAAGGTTAAAG
             tgttaat  putative branch site (score: 3)
                                      ctcttttgcttgctc  putative PPT
       tatgaatgttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaactttggggtgtcaattgtcaacatcagaaaagcatacttttgtcttagcacaattgttttgtttgaactttgttatattctaatacgaacaatatcgccagtgcctatgaatgttaattattcttctgaattcacgctcttttgcttgctcagTTCTGGTGATGTTCGTGTGAATTGGACACCAACAACAAAAAATGGAGTTACCCTCAAATCTGGAGATGTTGTTTCTGTTAGTGGGATGGGAAGGTTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG