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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttgtttccatttattctttgattctctaatgtaccaaatgcaatgcacggataagttgaagagttaaatgcataaggggtaccacttaggtcc...

Basic information

species Zea mays
transcript GRMZM5G818887_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g10290.2 (Oryza sativa), 5'ss of exon 7
TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttgtttccatttattctttgattctctaatgtaccaaatgcaatgcacggat-aagttgaag-agttaaatgcataaggggtaccacttaggtcc----
|||||||||||| ||| ||||||||||||||||||||| ||||||||||| || ||||| || |||||| |||    |||  |||| | |||| |  |   |||||  ||||| ||  || | || || |||||   | |   | ||  |        | ||  ||      
TCAAGAATGCCACTAAAGCCTGAACTTGTGTTTGAAGATATCAGCCAAGATCATGCACGGAAGACGgtactttca--ttcattttagtatttgctattgacatgta--aaatgaaa--catgaatcaacttgaactggattggttcaccaatatccttaattttgttagtac

upper sequence: GRMZM5G818887_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os10g41110.1 (Oryza sativa), 5'ss of exon 7
TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttgtttccatttattctttgattctctaatgtaccaaatgcaatgcacggat-aagttgaagagttaaatgcataaggggtaccacttaggtcc------
|||||||||||||||| ||||||||||||||||||||| |||||| ||||||| || || || ||||||||||    |||  || | | |||| |  |   |||||  ||||| ||  || | || || |||||  ||  | ||  | |    || |  |||  |        
TCAAGAATGCCATTAAAGCCTGAACTTGTGTTTGAAGATATCAGC-AAGACCATGCGCGGAAGACGgtattttca--ttcatttcagtatttgctattgacatgta--aaatgaaa--catgaatcaacttgaactgtggattggttcaccaatatc-tttaattttgttagt
















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|211435031|gb|FL327502.1|FL327502
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|86470328|gb|DY236698.1|DY236698
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|148960724|gb|EE011368.2|EE011368
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|18179571|gb|BM380781.1|BM380781
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|5525863|gb|AI861756.1|AI861756
EST:     TGCCTGAACTTGTGTTTGAAGCCATCAGTCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGAACATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|211295447|gb|FL439736.1|FL439736
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|78113030|gb|DV531424.1|DV531424
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|71313247|gb|DR793147.1|DR793147
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|148971663|gb|EE022386.2|EE022386
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|50331764|gb|CO526890.1|CO526890
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|78091451|gb|DV519825.1|DV519825
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|60342765|gb|DN209738.1|DN209738
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|76013820|gb|DT940990.1|DT940990
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|71313249|gb|DR793148.1|DR793148
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|60341702|gb|DN208675.1|DN208675
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAAGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|78091450|gb|DV519824.1|DV519824
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|211502356|gb|FL413772.1|FL413772
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCARTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|78022213|gb|DV490600.1|DV490600
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|211389689|gb|FL031640.1|FL031640
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|110482572|gb|EE011367.1|EE011367
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|60393918|gb|DN226788.1|DN226788
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|37374451|gb|CF623583.1|CF623583
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTTTTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|78113031|gb|DV531425.1|DV531425
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGAC
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGAC
EST: gi|101388963|gb|EB816463.1|EB816463
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|78077260|gb|DV505694.1|DV505694
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|76016276|gb|DT943446.1|DT943446
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|76016277|gb|DT943447.1|DT943447
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
EST: gi|15100603|gb|BI396394.1|BI396394
EST:     TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACG                         GTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG
genomic: TGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTG

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: 119

TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 212

TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 290

TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 152

TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttg ... attggcacagGTGACTATTGAGGACCATCCTCACTTATTGGCTGGGAAGCATGCATCAGTGCACCCATGCAAACATGCAGCTGTGATGAAAAAGATCATCGACGTTCCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAGAATGCCATTAATGCCTGAACTTGTGTTTGAAGACATCAGCCAAGACCACGCACGAAAAACGgtattttttgtttccatttattctttgattctctaatgtaccaaatgcaatgcacggataagttgaagagttaaatgcataaggggtaccacttaggtcc

- - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - TGAAGA