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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgcccttcgcttcatatcgatctgtgtatgccgcaggggatcctgccgtagatttggcgcggggatggcgttgcgggcctaggttttcgcttggatc...

Basic information

species Zea mays
transcript GRMZM2G374881_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g53060.2 (Oryza sativa), 5'ss of exon 1
GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgcccttcgcttcatatcgatctgtgta--tgccgcaggggatcctgccgtagatttggcgcggg---gatggcgttgcgggcctaggttttcgcttggatc
|||   || ||| |||||||||||||||||||||||||||| ||||| ||||||||||| || ||||||||||||| ||| ||||||||||||||||| |||| |||  |||   | |  ||||  | |      |  |    |||   |  |  | |||  || ||    | |||||| ||||||| |  ||||       |  
GACAATCCCACCTCCGGGGAGCACCGGATGGGGACCACCATCGTCGGCGTCTGCTACGACGGCGGCGTCGTCCTCGCCGCCGATTCCAGAACCAGCACCGgtatgcc--tcgacacctcccgatgcgggagatctcttccattgatgtggttg-gggtttaacgtggagccggtggcgtcgcgggcccaa-ttttgatgcaaaa-

upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g04800.1 (Oryza sativa), 5'ss of exon 1
GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccct-----tcgcttcatatcgatctgtgtatgccgcaggggatcctgccgtagatttggcgcggggatggcgttgcgggcctaggttttcgcttggatc
|||||||| ||| |||||||||||||||||||||||||||| ||||| ||||||||||| || ||||||||||||| ||| || ||| | |||||||| ||||||| |      || |       ||||| |    |     | |  |   ||| || |||||   |     |  || |   |  |||    |    | ||    
GACGCCCCCACCTCCGGGGAGCACCGGATGGGGACCACCATCGTCGGCGTCTGCTACGACGGCGGCGTCGTCCTCGCCGCCGACTCCCGGACCAGCACCGgtacgctcccccgatcccccacccccgatccgacccttgtttatgctaggttgcggtggatttt-tgttattagcgcatctggttcctgccatccatcctg----

upper sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv04s0008g02850.t01 (Vitis vinifera), 5'ss of exon 1
--GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgcccttcgcttcatatcgatctgtgtatgccgcaggggatcctgccgtagatttggcgcggggatggcgttgcgggcctaggttttcgcttggatc----
   | |  ||      |   |  ||||  ||||| || || ||  | || |||  |||| | ||||| |||||||||||||| || |||||||||||||||||||| | | ||| || || |   ||| |  || |       | |      | | |    | |     ||          |  | | || |   ||  ||     
GTAATGGACCTGAATGCACCGCACACC--ATGGGAACGACTATCATTGGAGTCACCTACAATGGTGGTGTCGTCCTCGGCGCCGACTCCAGAACCAGCACTGgtaccctcctcgttttattt---tct-taaattctctgtttggttgctgagaaaagaaagagaatatataaaacaaaaagtttggattcttttttaaatttctt

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|211274177|gb|FK988507.1|FK988507
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211272373|gb|FK988497.1|FK988497
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274173|gb|FK988503.1|FK988503
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|50338298|gb|CO533424.1|CO533424
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274171|gb|FK988501.1|FK988501
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274176|gb|FK988506.1|FK988506
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|78109399|gb|DV527815.1|DV527815
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|91049302|gb|EB159720.1|EB159720
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211272372|gb|FK988496.1|FK988496
EST:     TGCTACGAGGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: TGCTACGA-GGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274179|gb|FK988509.1|FK988509
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|20803190|gb|BQ294240.1|BQ294240
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGGACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|76915113|gb|DV165828.1|DV165828
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211272370|gb|FK988494.1|FK988494
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274172|gb|FK988502.1|FK988502
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|91872633|gb|EB402590.1|EB402590
EST:     TCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: TCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211272369|gb|FK988493.1|FK988493
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274170|gb|FK988500.1|FK988500
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|211274174|gb|FK988504.1|FK988504
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
EST: gi|148967409|gb|EE018635.2|EE018635
EST:     CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTG                         GAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA
genomic: CTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACA

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: 294

GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 260

GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 262

GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgccctt ... tccaactcagGAATGTATGTAGCCAACCGTGCTTCAGACAAGATTACCCAATTGACAGACAATGTGTACGTTTGTCGCTCTGGATCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGCCCCGACCACCGGGGAGCACCGGATGGGGACCACCATTGTCGGGGTCTGCTACGAGGGTGGCGTCGTCCTCGGCGCTGATTCCAGAACCAGCACTGgtacgcccttcgcttcatatcgatctgtgtatgccgcaggggatcctgccgtagatttggcgcggggatggcgttgcgggcctaggttttcgcttggatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttcgc