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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatgcaacatgtatctgcctgcag

Basic information

species Zea mays
transcript GRMZM2G002807_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g36450.1 (Oryza sativa), 5'ss of exon 6
CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatg-caacatgtatctgcctgcag
|||||||| |||||||||||||||||||| |||||| |||||||||| |||||||| ||||||||||| || ||||||| |||||||||||||||||||||||| | || ||||||||| ||  |  ||  || |||     | ||  ||  |  |          | |||||| |    ||| ||| |  ||||||||   ||| | |||
CAAAATGTAAAGGTTATTGCCTGCATAGGGGAGCTGTTGGAAGAGAGAGAAGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaatt-cttcatcttgagttaaattaataatgg-----ttgatgagcctaca----------tcatctgaagacaagattcatgtatcaacatgt---tgctttcag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os09g36450.2 (Oryza sativa), 5'ss of exon 6
CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatg-caacatgtatctgcctg-cag
|||||||| |||||||||||||||||||| |||||| |||||||||| |||||||| ||||||||||| || ||||||| |||||||||||||||||||||||| | || ||||||||| ||  |  ||  || |||     | ||  ||  |  |          | |||||| |    ||| ||| |  ||||||||  ||  | | |||
CAAAATGTAAAGGTTATTGCCTGCATAGGGGAGCTGTTGGAAGAGAGAGAAGCAGGGAAAACTTTTGACGTCTGTTTTAAGCAGATGAAGGCTTTTGCAGgtgacaatt-cttcatcttgagttaaattaataatgg-----ttgatgagcctaca----------tcatctgaagacaagattcatgtatcaacatgttgctttcagacag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA19G36990.2 (Glycine max), 5'ss of exon 6
CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtga--aactttcttcatcttaagaaactttttta---ttggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatgcaacatgt-atctgcctgcag------
|||  | ||   || ||||| ||||| |||||  || | ||||| |||||||| || |||||||||||||| ||||||  |||  ||||||||| |||||||     |  || |   |||||   ||    ||||   || |  ||||   ||  || | ||  |   |        ||  || || |  || ||||  |  |  | ||||   |       
CAAGGTCTTGGAGTGATTGCATGCATTGGAGAATTGTTAGAAGAAAGGGAAGCTGGAAAAACTTTTGATGTTTGTTTTCAGCAATTGAAGGCTTATGCAGgtagtggaagttatgtttcttatataatccatttaaaattcgttttcttttgat-ttagaagaaacaaaaggggaaggatttggtggttgat-tgcattacatcgtttgccattatttacag

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA10G06740.1 (Glycine max), 5'ss of exon 6
CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaactttcttcatcttaagaaacttt-tttattggcattctaga---gaagtttgtaggcattgatttaatctgaggtgttgatgcatatgcaacatgtatctgcctgcag
 |   | |    || || || || || || || ||| |  |||| || ||||| || |||||||| ||||| ||||||  |||  ||||||||||||||||||||| ||| |   | ||   ||  ||  |||||   || | |  |    || ||| ||  |  | |    |||  |  |  ||||   ||||  || | |            
GAGGGTCTGGGTGTGATAGCATGTATTGGGGAACTGTTACAAGAAAGAGAAGCTGGGAAAACTTTCGATGTTTGTTTTCAGCAATTGAAGGCTTTTGCAGgtgaaagtttatatttatttgtaagtttaatttatatacactgtcaatataaattttttacactattaaccgatcaaaaatcatgataggtatg--actttt------------

upper sequence: GRMZM2G002807_T01 (Zea mays), 5'ss of exon 6
lower sequence: Vv03s0038g01780.t01 (Vitis vinifera), 5'ss of exon 6
CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgagg---tgttgatgcatatgcaacatgtatctgcctgcag---------
||   | |||| || || || || || ||||| ||| |  |||| ||||||||||| |||||||||||||| ||||||  ||| |||||||||||||||||  |     |  || |  | |    || |||     | | | ||  |  ||||   ||   |  | | |   |||    ||||||  | | || |||||   |||   |  |          
CAGGGTCTTAAAGTAATAGCTTGTATTGGAGAACTGTTACAAGAAAGGGAAGCAGGAAAAACTTTTGATGTCTGTTTTCAGCAAATGAAGGCTTTTGCAGgcaag----ttctcttgctgatgttctctttctcatggaatgtactgtcgttttgtggtcctcttgtgaaaagagaacttgttgactcttttgtaacatcgctcttgttcaatcatgcgcag

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|211221686|gb|FL287482.1|FL287482
EST:     GCAGGCAAAACTTTTGATGTATNGTTT-AGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAAGCCTGTTTGG
genomic: GCAGGCAAAACTTTTGATGTAT-GTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGA-GCCTGTTTGG
EST: gi|211221681|gb|FL287477.1|FL287477
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|71432049|gb|DR813099.1|DR813099
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|71432050|gb|DR813100.1|DR813100
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|29544708|gb|CB605088.1|CB605088
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|74237679|gb|DT645593.1|DT645593
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|74234869|gb|DT642783.1|DT642783
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|76283252|gb|DV022820.1|DV022820
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGTTTTTGCAG                         ATAGTATTTCAAAC
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAAC
EST: gi|21760201|gb|BQ635742.1|BQ635742
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGG
EST: gi|5268718|gb|AI770682.1|AI770682
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGGAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|74244594|gb|DT652508.1|DT652508
EST:     AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: AGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
EST: gi|31664075|gb|CD573255.1|CD573255
EST:     GCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAG                         ATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG
genomic: GCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGG

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: 48 (upstream exon), 49 (downstream exon)
Score: 114

CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 160

CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaacttt ... ctgcctgcagATAGTATTTCAAACTGGGCAGATGTTGTAATTGCATACGAGCCTGTTTGGGCTATTGGAACCGGAAAAGTTGCTACTCCTGAACAAGCCCAGGAAGTTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAATGTTAAGGTTATTGCCTGCATAGGAGAGCTGCTGGAAGAGAGGGAAGCAGGCAAAACTTTTGATGTATGTTTTAGGCAGATGAAGGCTTTTGCAGgtgaaactttcttcatcttaagaaacttttttattggcattctagagaagtttgtaggcattgatttaatctgaggtgttgatgcatatgcaacatgtatctgcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG