Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttcttgaatggtgatataacctgtttgcttacaatcaatttattcaatcaagtttctgctaatggtgcttactgatcacaaaactcccaactg...

Basic information

species Zea mays
transcript GRMZM2G000718_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000718_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 5'ss of exon 7
GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttcttgaatggtgatat--aacctgtt-tgcttacaatcaatttattcaatcaagtttctgctaatggtgcttactgatcac---aaaactcccaactg----------
||||| |||||||| |||||||||||| |||| ||||||||| ||||  |||| |||||||||||| | | ||| | | ||  |||    | | | |   |    | |  | |   | ||   | || ||     | |   | |||   |||| || |               
GTTGTTGCACAAACCGTTGAAGTTGGATCTCAAACTGCTGCAGCTCTATCACAACAAgtaagttttttgggatgataaaattcaacagaatattccttggacgtttcttgttagaaaggtcagtcctgataagtttaatccagcaccctaaaattctctttacatccttttag
















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|148993115|gb|EE033715.2|EE033715
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|211130915|gb|FL136653.1|FL136653
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|6022470|gb|AW067503.1|AW067503
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60354623|gb|DN221596.1|DN221596
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|30088412|gb|CB886617.1|CB886617
EST:     TGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         CCGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: TGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|149002889|gb|EE038886.2|EE038886
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAT                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60346808|gb|DN213781.1|DN213781
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAATTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|148941490|gb|EC886419.2|EC886419
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|37420501|gb|CF647941.1|CF647941
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60398834|gb|DN231650.1|DN231650
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|33466594|gb|CF243643.1|CF243643
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|28985028|gb|BQ539307.2|BQ539307
EST:     CTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|71327359|gb|DR800293.1|DR800293
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60349330|gb|DN216303.1|DN216303
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|148993116|gb|EE033716.2|EE033716
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|50333643|gb|CO528769.1|CO528769
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCCCTTTTCC
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60345394|gb|DN212367.1|DN212367
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|149112851|gb|EE295664.2|EE295664
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCA
EST: gi|60352046|gb|DN219019.1|DN219019
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|149009782|gb|EE041679.2|EE041679
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|78117925|gb|DV536312.1|DV536312
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|149089650|gb|EE178904.2|EE178904
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|211386633|gb|FL468002.1|FL468002
EST:     CMCAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAAYTYTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|78083753|gb|DV512146.1|DV512146
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|91869534|gb|EB400432.1|EB400432
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCCATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|71327358|gb|DR800292.1|DR800292
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60344730|gb|DN211703.1|DN211703
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|149074291|gb|EE162669.2|EE162669
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|33466593|gb|CF243642.1|CF243642
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCCCTTTTCC
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|50333644|gb|CO528770.1|CO528770
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|211130916|gb|FL136654.1|FL136654
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
EST: gi|60343169|gb|DN210142.1|DN210142
EST:     CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAA                         ACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA
genomic: CACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCA

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: 347

GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 172

GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG


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

GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 224

GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttc ... tttttttcagACGGAACAAATGAAGAGGATAGGCAATGAGCTAGATTCTGTCCACTTTTCACTGAAGAAGGCTAGTCAAATGGTGAAAGAGATTGGCCGTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTAGCACAAACTGTTGAAGTTGGAGCTCAGACTGCTGCAACTCTGACACAGCAAgtaagttttcttgaatggtgatataacctgtttgcttacaatcaatttattcaatcaagtttctgctaatggtgcttactgatcacaaaactcccaactg

- - - - - - - - TTGAAG
- - - - - - - - - - - TTGGAG
- - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaaac