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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCCCTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgcatctcagccccttgcgcaagttccctttttattcctgcattcctgattattcgataaggagttcaggactagtcgaaacgtaaaagcaaa...

Basic information

species Zea mays
transcript GRMZM2G032944_T02
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G032944_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g23169.1 (Oryza sativa), 5'ss of exon 1
TCCCCCTTTCTCGACC-CCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgca-tctcagccccttgcgcaagttccctttttattcctgcattcctgattattcgataaggagttcaggactagtcgaaacgtaaaagcaaa-----
      |  | |||||  || | ||      ||  ||||||||| |||  | |||||||||||||  |||||||||||||||||  | | ||| || || || |||||| || |||| || |    | |   | ||||    |   |||   || |  || ||   |  ||| | |   | | ||    |  ||  |          
------TCCCACGACCGTCGGCACCCCGGAGACGCCGCCGCCGCCGCCGCCCTCGGAGGCCTGGACGAGCTTCCACCGTCGCCACACATGCGGCAAGTTTTTCAAGgtttcaatctccgctctcctccctgttaccctgcgcagatctgtcgtc-tactttttttttccggactgcgcaaatcgttaggaattaggatttctattgt
















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|211385267|gb|FL300399.1|FL300399
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|37417157|gb|CF646231.1|CF646231
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|211385272|gb|FL300404.1|FL300404
EST:     TCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTT
genomic: TCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGT-CCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTT
EST: gi|211387892|gb|FL300408.1|FL300408
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|93284543|gb|EB676807.1|EB676807
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|71765663|gb|DR963600.1|DR963600
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|211385274|gb|FL300406.1|FL300406
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGG
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGG
EST: gi|78116629|gb|DV535016.1|DV535016
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|211385269|gb|FL300401.1|FL300401
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|78124012|gb|DV542396.1|DV542396
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|91047980|gb|EB158398.1|EB158398
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|149085005|gb|EE174515.2|EE174515
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|71448268|gb|DR829318.1|DR829318
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|76014696|gb|DT941866.1|DT941866
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|93284224|gb|EB676488.1|EB676488
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|76914812|gb|DV165698.1|DV165698
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|31355055|gb|CD439412.1|CD439412
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|211385273|gb|FL300405.1|FL300405
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGC
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGC
EST: gi|71438631|gb|DR819681.1|DR819681
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTC-                         -TTTA-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
EST: gi|211385271|gb|FL300403.1|FL300403
EST:     GTCGGARGCCTGGAGAAGCTTCCACCGTCGCCATGTGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAA
EST: gi|89761751|gb|DY689640.1|DY689640
EST:     GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCT                         TT--A-AGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA
genomic: GTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCA

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: 47 (upstream exon), 44 (downstream exon)
Score: 33

TCCCCCTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 52

TCCCCCTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 42

TCCCCCTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

TCCCCCTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgc ... ctgatattacTTTTACAGGAAAGGAGATATTTGCTTAAGGAATTTCCTGAACTTTGTAGCAGCAAAGATCATGCCAAGGTTTTAGAAGTGGGGTGTGGGAATGGAAGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCCCTTTCTCGACCCCGCCGCCAGTACCACCTCGCCGCCGCAGCCCTCGTCGGAGGCCTGGAGAAGCTTCCACCGTCGCCATGCGTCCGGAAAATTCTttaaggttgcatctcagccccttgcgcaagttccctttttattcctgcattcctgattattcgataaggagttcaggactagtcgaaacgtaaaagcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagcaa