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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagttttatcctttcag

Basic information

species Zea mays
transcript GRMZM2G009876_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g47580.1 (Oryza sativa), 5'ss of exon 5
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgct-tcaatgggttagtt---tttact---------cacagttttat-cctttcag
||||||||||||||||| ||||||||||||| ||||||||||||||||||||| |||||| |||||||||||||| ||||||||    |    |      | ||  ||||||| ||   |   || |||         |||| |||| | ||||||||
GTTCTCAGCAACACAATTAAGCAAAAGAGGATGGAAAAGGCTGGCAAATGGGAGGTTCCTTTGCCAAAGgtgattttcaacacaaactgtttctagtacctggcaatcaatggttttcctaccttgactaagcactgtcacaattttcttcctttcag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G10000.1 (Glycine max), 5'ss of exon 5
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtga-----ttctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagttttatcctttcag-------------------------------------------------------------------------
||||| ||||||||||| ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||        |||| ||     ||    |  |   || |    |  |  |  | |  || |  | | | || | |  |                                                                         
GTTCTTAGCAACACAATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattacgttcaatactttgtgcattatgttaaatgatatcttttgcaatgtgtatcttattgctatttcatgtttgttttatgtttccctgtgaatggaagggagcgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA10G00490.1 (Glycine max), 5'ss of exon 5
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgcttcaatgggttagtttt-tactcacagttttatcctttcag---------------------------------------------------------------------------------
||||| |||||||| || ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||   |     ||  ||         || ||   | ||  | |  || ||  | |     | ||||   |                                                                                     
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCGGGAAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttgtgcattgattatgttaaatgatatgtcttgcaatttgtatcttattgctatgtcatgtgtgttttatgtttccctgtgaatggaagggagtgaacttggtaattaaatgaatgtatgctttctcatttcttcag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA02G35500.1 (Glycine max), 5'ss of exon 5
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagttttatcctttcag------------------------------------------------------------------------------------
||||| |||||||| || ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||   |     ||  ||        | | ||   | ||   | ||  | || |     |||   |  ||  |                                                                                     
GTTCTTAGCAACACCATTAAGCAAAAGAGGAAGGAGAAGGCAGGGAAATGGGATGTTCCTCTACCTAAGgtgaaattgcgttcaatactttttgcacggattatgttaa-acgatatctcttgcaatttgttccttgtttctatttcatgtgtgttttatgtttccctgttaatggaagggagcgagcttgagtaattaaatgaatgtatactttctcatttcttcag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT5G06360.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtga-------ttctcaac----acagcacgcccatttctggttgct--tcaatgggttagtttttactcacagttttatcctttcag--
||||| |||||||| || || ||||||||||| || || |||||||||||||| || ||||| ||||||||||        ||||  |      |   |  |  | | ||    ||    ||||||  |   || | |   ||   | |||||| |   
GTTCTTAGCAACACCATTAAACAAAAGAGGAAAGAGAAAGCTGGCAAATGGGAGGTCCCTCTTCCAAAGgtgaaatctctctctctgcttttgtattccttcagtgtttgaactctaacaaatgggcaaagcttaaattcaagccctgtccttttacag

upper sequence: GRMZM2G009876_T01 (Zea mays), 5'ss of exon 5
lower sequence: PP1S136_220V6.1 (Physcomitrella patens), 5'ss of exon 5
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagt-tttatcctttcag---------------------------
|||||||||||||| || ||||| ||  | ||||| |||||||| |||||||| || ||||| || |||||||  |   | |  | |||     |   | ||| |  ||    | | |  |    ||||    |||   | | |                            
GTTCTCAGCAACACCATCAAGCAGAAACGTAAGGAGAAGGCTGGTAAATGGGAGGTGCCTCTTCCTAAGgtgagcc--gatatcgtacgaatgctgtagcttg-tgaaactcttgaataatccaccacatcacttaaattgtgaagtacgtgaacggaggcgatgtggtttc

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|211143002|gb|FL390386.1|FL390386
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|24764520|gb|CA399684.1|CA399684
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|101382315|gb|EB813213.1|EB813213
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|74232800|gb|DT640714.1|DT640714
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|211129107|gb|FL371425.1|FL371425
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAA-TGTTCA-GGTTCTACGGACTGGC
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGC
EST: gi|101390908|gb|EB817389.1|EB817389
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAAAAATGTTCAAGGTTCTACGAACTGGCCAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|6918424|gb|AW399954.1|AW399954
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGGACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|74232799|gb|DT640713.1|DT640713
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|67038385|gb|CO464715.1|CO464715
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|101392350|gb|EB818104.1|EB818104
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCAAAAG                         GTCAGGCCTGTAGCTGA
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGA
EST: gi|211049010|gb|FL423464.1|FL423464
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGGACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|211358243|gb|FL402304.1|FL402304
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|148953095|gb|EE152575.2|EE152575
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|29946116|gb|CB815987.1|CB815987
EST:     TGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: TGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|31350057|gb|CD434414.1|CD434414
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|211133673|gb|FL369483.1|FL369483
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAA-TGTTCAAGGTTCTACGGACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|60399997|gb|DN232804.1|DN232804
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|76015209|gb|DT942379.1|DT942379
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCANGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|60351247|gb|DN218220.1|DN218220
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|88757436|gb|DY541577.1|DY541577
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|4776075|gb|AI665078.1|AI665078
EST:     GCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: GCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|149027253|gb|EE046450.2|EE046450
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAG
EST: gi|211300841|gb|FL383944.1|FL383944
EST:     AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAG                         GTCAGGCCTGTAGCTGAAGA
genomic: AGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 147

GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 155

GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 101

GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctca ... atcctttcagGTCAGGCCTGTAGCTGAAGAAGAAATGTTCAAGGTTCTACGAACTGGCAAGCGAAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCTCAGCAACACAATAAAGCAAAAGAGGAAGGAAAAGGCTGGCAAATGGGATGTTCCTCTGCCAAAGgtgattctcaacacagcacgcccatttctggttgcttcaatgggttagtttttactcacagttttatcctttcag

- - - - - - - - - - - - AAGAGG
- - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - AAGGAA