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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactaccttttctattggaattttgtcaacgtacatgttaacgtttgcaaagaatttgcaagtcgtcacgaaccattttgtggtttatgactgacga...

Basic information

species Zea mays
transcript GRMZM2G087598_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G087598_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g45820.1 (Oryza sativa), 5'ss of exon 4
CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactac-cttttctattggaattttgtcaacgtacatgttaacgtttgcaa-----agaatttgcaagtcgtcacgaaccattttgtggtttatgactgacga
|||||| ||| | |||||||||||| |||| ||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||  |||   || | |  | ||| ||||  ||   |  |    |   ||  ||     ||| | || ||   ||   |  |   |      |||||||||     
CCTTGGCGGTCGTGCTGCTGAGGAGATCATTTTTGGGGAGCCTGAGGTGACCACAGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCCTAGCCAAGCAGgtacgctatatttctattctagaactttgctaattgatctacagaaactttgaagcagtagactatgtaatctgttctg--cttctgcaccttttatgactt----

upper sequence: GRMZM2G087598_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G17070.1 (Glycine max), 5'ss of exon 4
CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactaccttttctattggaattttgtcaacgta-catgttaacgtttgcaaagaatttgcaagtc-gtcacgaaccattttgtggtttatgactgacga
 ||||| || ||||| || ||||| || || ||||| ||||||||||| || |||||||| |||||||| ||||||||||| ||  | || |||||||||||       | |  || |      | | | || ||| ||  ||    ||          |||| | || |       |  |  ||     ||  | |||   
ACTTGGGGGCAGAGCAGCAGAGGAAGTTATTTTTGGTGAGCCTGAGGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATAACCAGTTTGGCCAAGCAGgttggtgttcatgactttattttctgttttaatgtatcacatttctcttgttctctttcttgctattctgcttttggcggtgatgaatgctagcagtgat--

upper sequence: GRMZM2G087598_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G26230.1 (Glycine max), 5'ss of exon 4
CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactaccttttctattggaattttgtcaacgtacatgttaacgtt-tgcaaagaatttgcaagtcgtcacgaa---ccattttgtggtttatgactgacga
 || ||||| || ||||| || ||  | || ||||| |||||||| || || |||||||| |||||||| ||||||||||| || || || || || |||||||  |   |  |    ||   || ||| |    | || |     || |  |    ||||    || ||    ||   | | | | |    ||  | ||    
ACTAGGTGGAAGGGCTGCAGAAGAAATTATTTTTGGTGAGCCTGAAGTTACAACTGGAGCAGCTGGTGATTTGCAGCAAATCACCGGTTTGGCAAAACAGgtat--tggttaattatgtgcttttgtgttacaaaatatctcctttttctttattttatttttgtgtggtggaaaatgcctaatatttatggtaatattgtt--

upper sequence: GRMZM2G087598_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT1G06430.1 (Arabidopsis thaliana), 5'ss of exon 4
CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtata----ctaccttttctattggaattttgtcaacgtacatgttaacgtttgcaaagaatttgcaagt-cgtcacgaaccattttgtggtttatgactgacga
 || |||||||||||||| || || ||||| ||||| ||| |||||||||| ||||| || | | |||||||||| || || || || || || ||||||||||     ||||  |  |   |  | | || |   |    ||  |||  |    || ||| |||  |||   |||  |   | || |  |              
ACTCGGTGGTAGAGCTGCCGAAGAAGTCATCTTTGGTGAGTCTGAGGTGACTACTGGTGCAGTTAGTGACTTGCAACAGATCACCGGTTTGGCTAAGCAGgtatctcttctacactcccagcttcagtatttttttctgttatcctaaactagtgaatgaacttgacagtatatcatcatttactt-gcag--------------

upper sequence: GRMZM2G087598_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 5'ss of exon 4
CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtat--actaccttttctattggaattttgtcaacgtacatgttaacgtttgcaaagaat-ttgcaagtcgtcacg---aaccattttgtggtttatgactgacga
 || ||||| ||||||||||| || || || ||||| |||||||||||||| || || ||||||||||| |||||||| || ||||| || ||||| ||||||   |  |  |  || ||  |  |   |       |||| | |||   ||||||     |||  |||    |     |||   |         |  ||   |  
ACTCGGTGGCAGAGCTGCTGAAGAAGTGATCTTTGGTGAGCCTGAGGTGACAACAGGTGCTGCTGGTGATTTGCAGCAGATCACTGGTTTGGCCAAACAGgtaataaacagttcctccatctgcttccagctggta-acatttaaac---tgcaaatgtcattgtcagtttctattctcaacatatacaaaacacagtaccacc--

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|78090967|gb|DV519341.1|DV519341
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|5468910|gb|AI834701.1|AI834701
EST:     TGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: TGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|13315943|gb|BG410291.1|BG410291
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|24934237|gb|CA452455.1|CA452455
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|74235282|gb|DT643196.1|DT643196
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|4688537|gb|AI637207.1|AI637207
EST:     TGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGGGTTGTGACCATTCGGTATGTCTGAAATTGGTCCATGGGTCTCTGAT
genomic: TGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagAT--GGTTGTGA-CATTCGGTATGTCTGAAATTGGTCCAT-GGTCTCTGAT
EST: gi|83279003|gb|DV943011.1|DV943011
EST:     TAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: TAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|149086842|gb|EE176390.2|EE176390
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|5081174|gb|AI738331.1|AI738331
EST:     CTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|211130727|gb|FL008628.1|FL008628
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTG--A--C---AT-TC-GAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|24934160|gb|CA452378.1|CA452378
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|149089171|gb|EE178359.2|EE178359
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTGAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|32866642|gb|CF006324.1|CF006324
EST:     GGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: GGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|76011445|gb|DT938615.1|DT938615
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|78076092|gb|DV504526.1|DV504526
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|5757145|gb|AI964432.1|AI964432
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|88754818|gb|DY538959.1|DY538959
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|37377001|gb|CF625070.1|CF625070
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|4730570|gb|AI649736.1|AI649736
EST:     TGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: TGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|50334510|gb|CO529636.1|CO529636
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|5468966|gb|AI834757.1|AI834757
EST:     CACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|33467965|gb|CF245014.1|CF245014
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|13178114|gb|BG349372.1|BG349372
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|211188746|gb|FL459413.1|FL459413
EST:     CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: CCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
EST: gi|13177829|gb|BG349177.1|BG349177
EST:     GAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAG                         ATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG
genomic: GAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAG

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: 45

CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAGGGTGGAGCGCAGAGTGGGGACGTCATCATGAGAATGATGGCAAGGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAGGGTGGAGCGCAGAGTGGGGACGTCATCATGAGAATGATGGCAAGGAACT


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 35

CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAGGGTGGAGCGCAGAGTGGGGACGTCATCATGAGAATGATGGCAAGGAACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactacc ... ggttctgcagATGGTTGTGACATTCGGTATGTCTGAAATTGGTCCATGGTCTCTGATGGAGGGTGGAGCGCAGAGTGGGGACGTCATCATGAGAATGATGGCAAGGAACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTGGTGGTAGAGCTGCTGAGGAGGTCATATTTGGAGAGCCTGAGGTGACCACTGGAGCTGCTGGTGACTTGCAGCAAATTACTGGCTTAGCCAAGCAGgtatactaccttttctattggaattttgtcaacgtacatgttaacgtttgcaaagaatttgcaagtcgtcacgaaccattttgtggtttatgactgacga

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT