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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccgaaatatcttttctaaaatcattgtacctatcttgtttatcttggtttgatctgatatcatttttatgttcgtaccaactactctaaataaattaagctctttccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA

Basic information

species Zea mays
transcript GRMZM2G126517_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126517_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g39420.1 (Oryza sativa), 3'ss of exon 4
----gtgccgaaatatcttttctaaaatcattgtacctatcttgt-ttatcttggtttgat----------ctgat-atcatttttat-----gttcgtaccaacta-----ctctaaat--aaattaagctctttccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA
    | ||| |||     || ||    |  ||     ||  || | ||  |||| ||||||           || | ||| || |||      ||| || ||||  |     ||||| ||  || | ||| |  |  ||||||||||||||||||||| |||| || ||||| || ||||||||||| |||||| |||||||||| |
gtcagagccaaaaacatcttactgctcttgttactgttaatttatctttccttgatttgatagcctttttcttgttcatctttgttacatgtagttggtgccaatcattcatctctatatcaaactaaagttgctctcaaattcagGTTGGCATACCAATTTTCGTAACTGGAGGGATTGGAGGTGTTCATAGAAATGGTGAACAGA

upper sequence: GRMZM2G126517_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0009g02380.t01 (Vitis vinifera), 3'ss of exon 5
gtgccgaaatatcttttctaaaatcattgtacctatcttgtttatcttggtttgatctgatatcatttttatgttcgtaccaactactctaa-ataaattaagctctttccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA
  |    ||      |  ||   |  |   |  ||     |  || ||||  |  |||| || | ||  ||  ||  ||   | | |||| | |   |||||||          | |||||||||||||| || ||||||||||| || |||||||| || ||||||||||| ||  | |
--gtgacaactctgatcttagctttctcacagttactagatacatgttggcattttctg-taaccttaataatttgttatatatttctctcatagttattaagcaaaaaattcttacagGTTGGCATACCTGTCTTTGTTACTGGAGGAATTGGAGGAGTACATAGACATGGAGAGAATA
















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|211075732|gb|FL350793.1|FL350793
EST:     TGGCAACGGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGG
genomic: TGGCAACGG-CGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGG
EST: gi|67038503|gb|CO464823.1|CO464823
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211098559|gb|FL329018.1|FL329018
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGANGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|149082843|gb|EE172069.2|EE172069
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211522432|gb|FL327537.1|FL327537
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGANGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211469725|gb|FL319610.1|FL319610
EST:     GTNGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATWGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211193875|gb|FL364459.1|FL364459
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|149015839|gb|EE045506.2|EE045506
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211370472|gb|FL346947.1|FL346947
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTAC
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTAC
EST: gi|211152952|gb|FL361222.1|FL361222
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211177454|gb|FL359127.1|FL359127
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCAT
EST: gi|211327335|gb|FL364053.1|FL364053
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGA
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGA
EST: gi|211483892|gb|FL352027.1|FL352027
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACA
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTT-GTTACTGGGGGCATTGGAGGTGTGCATAGACA
EST: gi|211088384|gb|FL316163.1|FL316163
EST:     TGGCAACGGCGCAACAACAGTTTCGGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTG
genomic: TGGCAACGGCGCAACAACAGTTTCGG-CCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTG
EST: gi|211103326|gb|FL320696.1|FL320696
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGTGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|31355893|gb|CD440250.1|CD440250
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211385441|gb|FL308637.1|FL308637
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|78085709|gb|DV514102.1|DV514102
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211526420|gb|FL361968.1|FL361968
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGG
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGG
EST: gi|211023235|gb|FL319676.1|FL319676
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211115835|gb|FL357318.1|FL357318
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGT
EST: gi|211386536|gb|FL356614.1|FL356614
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211216455|gb|FL358323.1|FL358323
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211472964|gb|FL344042.1|FL344042
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTTGTTACTGGGGGC
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTT-GTTACTGGGGGC
EST: gi|211522504|gb|FL328840.1|FL328840
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTAC
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTAC
EST: gi|211267860|gb|FL346397.1|FL346397
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211229181|gb|FL350913.1|FL350913
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAC                         GTTGGCATACCAGTTTTT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTT
EST: gi|211370106|gb|FL332774.1|FL332774
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGG
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGG
EST: gi|211404920|gb|FL353800.1|FL353800
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGGCATAGACA
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTG-CATAGACA
EST: gi|211258208|gb|FL352264.1|FL352264
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGG
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGG
EST: gi|74236392|gb|DT644306.1|DT644306
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211338223|gb|FL361344.1|FL361344
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGC
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGC
EST: gi|211420492|gb|FL364949.1|FL364949
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|211526578|gb|FL367182.1|FL367182
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|31355559|gb|CD439916.1|CD439916
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|71764027|gb|DR961964.1|DR961964
EST:     GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
genomic: GTGGCAACGGCGCAACAACAGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACAT
EST: gi|101391313|gb|EB817591.1|EB817591
EST:     GGCAACGGCCGCA-CAACCAGTTTCGGCCACTATGTTCTTTGCTCACAAG                         GTTGGGC-TACCAGTTTTTGTTACTGG
genomic: GGCAACGGC-GCAACAAC-AGTTTCGGCCACTATGTTCTTTGCTCACAAGgtgccgaaat ... ccaaattcagGTTGG-CATACCAGTTTTTGTTACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttatgttcgtaccaactactctaaataaattaagctctttccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA
                       ctctaaa  putative branch site (score: 3)
                                       ctctttcc  putative PPT
                     tactctaaataaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgccgaaatatcttttctaaaatcattgtacctatcttgtttatcttggtttgatctgatatcatttttatgttcgtaccaactactctaaataaattaagctctttccaaattcagGTTGGCATACCAGTTTTTGTTACTGGGGGCATTGGAGGTGTGCATAGACATGGTGAACAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG