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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactcttcctttcttgtcttgttactgtattgttttcccgatttgctcgttgtggactgatatctgcatcactttcttcatacgtttgtatttccc...

Basic information

species Zea mays
transcript GRMZM2G065757_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065757_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 5'ss of exon 2
ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactctt-----cctttcttgtcttgttactgtattgttttcccgatttgctcgttgtggactgatatctgcat-cactttcttcatacgtttgtatttccc
|| || |||| ||||||||| ||||||||||| || ||||| ||||||||  ||||||| |||  |   |||       |  |    | || || | ||| ||| |  |  | |||   |    |  |   |  || || || |  |  ||| | ||| |  |    
ATTGCGTGCTTCTTCCACTCTCGCTACAAGTCCGGACAGTCGAGCACTTATCAGAAGAATGgtccgtgccttaaaactttccccaaccgtgctagtttat-gttgtgactgtctgcctctctcagttt---acttggatgcattgacaacatccttttttgctat--
















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|31440937|gb|CD510368.1|CD510368
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTG
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTG
EST: gi|29576941|gb|CB617053.1|CB617053
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTG
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTG
EST: gi|149095835|gb|EE181486.2|EE181486
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|149078470|gb|EE167250.2|EE167250
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|32830382|gb|CD970060.1|CD970060
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|32840007|gb|CD979688.1|CD979688
EST:     CTTCCACTCGCGCTACAAGGCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|32850768|gb|CD990449.1|CD990449
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTACTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|211063419|gb|FL406486.1|FL406486
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAA
EST: gi|211314123|gb|FL216094.1|FL216094
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCAT
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCAT
EST: gi|50338072|gb|CO533198.1|CO533198
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|32839505|gb|CD979186.1|CD979186
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|211514658|gb|FK981816.1|FK981816
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGTTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|32839962|gb|CD979643.1|CD979643
EST:     CTTCCACTCGCGCTACAAGGCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|32839693|gb|CD979374.1|CD979374
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|148956524|gb|EC902364.2|EC902364
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|211092714|gb|FK945554.1|FK945554
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGC
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGC
EST: gi|211312095|gb|FL216082.1|FL216082
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|148931369|gb|EC874278.2|EC874278
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
EST: gi|33099258|gb|CF059218.1|CF059218
EST:     CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACG                         GAAAACCTGCTGCCATTCGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA
genomic: CTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCA

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: 836

ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1369

ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 901

ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1048

ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactct ... aactctctagGAAAACCTGCTGCCATACGCTATGGAACTGGTTCCATTGCTGGTTTTTTCAGTGAGGATAGCGTTACATTAGGTGATCTGGTTGTGAAGGATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGCTTGCTACTTCCACTCGCGCTACAAGTCAGGGCAGTCAAGCACTTACAAGAAGAACGgtttgactcttcctttcttgtcttgttactgtattgttttcccgatttgctcgttgtggactgatatctgcatcactttcttcatacgtttgtatttccc

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC