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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctcttaacactctgctaattcattttatgttcaacatgaggaaagaaaaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA

Basic information

species Zea mays
transcript GRMZM2G080375_T03
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080375_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g09570.1 (Oryza sativa), 3'ss of exon 8
gtacgctcttaacactctgctaattcattttat-gttcaacatgaggaaagaaaaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
||| | | | | || ||| ||  ||||||  || | ||||  |  || ||            ||   ||   |  ||  ||| |  | | || |      ||| |||||| ||||| |||||||| ||||| || ||||| || ||||| || || |||||||| || ||| ||||||  |||||||||||||| ||||| |||||||
gtatgttttaatcattctacttgttcattgcattgatcaatctagggtaa------------atgctgaattatatggttgatc--tacttttt------tacttcagGATTGTTGCTTAATCCCAGAGTCTCCATTCTATCTAGAAGGAAAAGGTGGACTCCTTGAATTCATCGAGAAACGGCTCAAGGACAATGGCCATATGGTCA

upper sequence: GRMZM2G080375_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 8
-------------------------------------gtacgctcttaacactctgctaattcattttatgttcaacatgaggaaagaaaaaatatatatag---cgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
                                         ||| || |   ||||   ||   |||  | | |    | | ||   | |  ||   |  ||     |    | ||| || ||||||  | ||| | |  |  |  ||||||||| || || || ||||||||||||||||| ||||| ||||| |||||  | ||                                         
taacaattgtaagtgtattttatcgtctaagtgcaccagttgcttttgaggatctg--gatctttttcttttcctgtgttatgatgaatactatgactgcagGTTTTATTGCAATGTATG-CCACTCT-TGCTAGCAGAGATGT--GGACTGTTGCTTGATTCCAGAGTCACCCTTCTACCTTGAAGGAAAGGGTGGACTTTTTGA-----------------------------------------
















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|116813643|gb|EC856113.1|EC856113
EST:     GTTTTATCGCGATGTACGCAACTCTAGCTAGCCGTGATGTG                         GACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGG
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGG
EST: gi|148980656|gb|EE027274.2|EE027274
EST:     GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG                         GACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGA
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGA
EST: gi|211450005|gb|FL281917.1|FL281917
EST:     GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG                         GACTGTTGTTTAATCCCGGAGTCACC
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACC
EST: gi|211450006|gb|FL281918.1|FL281918
EST:     GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTG                         GACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGA
genomic: GTTTTATCGCGATGTACGCGACTCTAGCTAGCCGTGATGTGgtacgctctt ... gctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA
                       gtctgac  putative branch site (score: 3)
                                              ctacctc  putative PPT
     atatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctcttaacactctgctaattcattttatgttcaacatgaggaaagaaaaaatatatatagcgagccaagtgtctgaccactccattctacctgctacctcagGACTGTTGTTTAATCCCGGAGTCACCCTTCTACCTCGAAGGGAAGGGAGGACTCCTCGAGTTCGTCGAGAGGCGGCTCAAGGACAACGGCCACATGGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG