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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttctcaatgagtcctttttgtcacatttttcaggattatcccattgtacaagtagttagatccttagaggtgtagtgataacctaacaagcctttgcaattagttgtgatgctatctatcaattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATCTGGGAGGAAATGAACAAAGAGTACCTTGAG

Basic information

species Zea mays
transcript GRMZM2G096389_T05
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096389_T05 (Zea mays), 3'ss of exon 13
lower sequence: Vv08s0056g01250.t01 (Vitis vinifera), 3'ss of exon 16
gtgctttctcaatgagtcctttttgtcacatttttcaggattatcccattgtacaagtagttagatccttagaggtgtagtgataacctaacaagcctttgcaattagttgtgatgctatctatcaattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATCTGGGAGGAAATGAACAAAGAGTACCTTGAG
                         |   || |||   ||| ||    |  | |    || || || ||    |||| | |  | |  |       | |||  | |   |||| |  || | ||  ||| ||||||||||||| || |||||||||||| | || |  |||| |||||||||||| ||||| | ||||||||| ||||||||||||
-----------------------aattgtatattt--agatgatgtattcatgc---cagctatatgctatacggtgcatt--tcattt--tggttcattg--actttgtgtggttatacc-atatattgtgtagGTTGATGGCTATCTTCACAATGAGAAGGAGAAGCAATTTAAAAAGATTATTTGGGAAGCAATGAACAAGGAGTACCTTGAG
















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|211368014|gb|FL470445.1|FL470445
EST:     AGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCCCAATGAGGAAGAAACCCAATATAAAAAGATTATC
genomic: AGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
EST: gi|211368015|gb|FL470446.1|FL470446
EST:     GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCACAATGAGGAAGAAACCCAATATAAAAAGATTATC
genomic: GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
EST: gi|211023732|gb|FL449221.1|FL449221
EST:     GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
genomic: GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
EST: gi|76018788|gb|DT945958.1|DT945958
EST:     GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
genomic: GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
EST: gi|78120367|gb|DV538751.1|DV538751
EST:     GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
genomic: GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
EST: gi|60396686|gb|DN229553.1|DN229553
EST:     GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
genomic: GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
EST: gi|211122767|gb|FL444236.1|FL444236
EST:     GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAG                         GTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC
genomic: GTGAAGGCAATGCAGATCCAGAAAGCCTTTCTGACATTGACGATGCAGAGgtgctttctc ... aattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataacctaacaagcctttgcaattagttgtgatgctatctatcaattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATCTGGGAGGAAATGAACAAAGAGTACCTTGAG
     acctaac  putative branch site (score: 2)
                                     tatctatcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttctcaatgagtcctttttgtcacatttttcaggattatcccattgtacaagtagttagatccttagaggtgtagtgataacctaacaagcctttgcaattagttgtgatgctatctatcaattttgtagGTTGATGGGTACCTTCACAATGAGGAAGAAACACAATATAAAAAGATTATCTGGGAGGAAATGAACAAAGAGTACCTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA