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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgccgactctgtgaaggcgtcgtcgtatttattgtgtgcctaaataagattagctatgcttggtgtttagtttaggactagaaaatctctacac...

Basic information

species Zea mays
transcript GRMZM2G000718_T01
intron # 9
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 9
lower sequence: LOC_Os07g44350.1 (Oryza sativa), 5'ss of exon 9
GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgccgactctgt-gaaggcgtcgtcgtatttattgtgtgcctaaataagattagctatgcttggtgtttagtttaggactagaaaatctctacac-----
||||| |||||||||||||| ||||| ||||| |||||||| ||||||||||| |||||||| |||||||||||||||||||       || | | |   ||   | | ||  ||     | ||  | | || |  | |   ||   |  |   |    ||| |   ||  ||        
GTTGCAACTGACAAATGCATCATGGCATTCCTATTTCTGATAGTCTGTGGTGTGATTGCAATCATTGTTGTTAAGgtatgttttaattgcttttgcaaatgtacccatgttgtttac---cttaggtgacatcacttgt---tgagataaaaactgatcctatatcctccgtatgtgcaag

upper sequence: GRMZM2G000718_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G04460.1 (Glycine max), 5'ss of exon 9
GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgccgactctgtgaag-gcgtcgtcgtatttattgtgtgcctaaataagattagctatgc--ttggtgtt-tagtttaggactagaaaatctctacac
|| ||||||||||| ||||| |||   || ||||| || |||||||||||||| ||||| || ||||| || |||||||| ||   | |   |  |   | | |  | |||| |||||    |   |    | |  ||  |  ||  ||||  | |||  ||  |  |||         
GTAGCTACTGACAAGTGCATCATGCTTTTTCTGTTCCTTATTGTCTGTGGTGTAATTGCCATTATTGTCGTGAAGgtatggtgttcatttcatccattactttgatgaatttgttgtggatatttttcctctcaaatagacaattactgttacaatttttgaaaattaaactaag----

upper sequence: GRMZM2G000718_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA17G04460.2 (Glycine max), 5'ss of exon 8
-------------------------GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgccgactctgtgaag-gcgtcgtcgtatttattgtgtgcctaaataagattagctatgc--ttggtgtt-tagtttaggactagaaaatctctacac
                         || ||||||||||| ||||| |||   || ||||| || |||||||||||||| ||||| || ||||| || |||||||| ||   | |   |  |   | | |  | |||| |||||    |   |    | |  ||  |  ||  ||||  | |||  ||  |  |||         
CTGAATTGTCTTTCCATGTTATCAGGTAGCTACTGACAAGTGCATCATGCTTTTTCTGTTCCTTATTGTCTGTGGTGTAATTGCCATTATTGTCGTGAAGgtatggtgttcatttcatccattactttgatgaatttgttgtggatatttttcctctcaaatagacaattactgttacaatttttgaaaattaaactaag----

upper sequence: GRMZM2G000718_T01 (Zea mays), 5'ss of exon 9
lower sequence: AT1G48240.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgccgactctgtgaaggcgtcgtcgtatttattgtgtgcctaaataagattagctatgcttggtgtttagtttaggactaga-aaatctctacac--
|| ||||| || |||||||| |||||||||||||||||||||||||||||||| || || |||||  |||| ||||||        |||||   |           |  | |||  | ||| ||||||   ||   || | |   |     ||||  |||    ||||    ||||  
GTAGCTACAGATAAATGCATAATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTTATAGCTATAATCATTGTGAAGgtaaccattgcactctccaa--------cttttctcattacg-gcccaaataaagcta-tgattccttaagcaagttttaacactgcttaaataaaaacacag

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:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|211130915|gb|FL136653.1|FL136653
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|6022470|gb|AW067503.1|AW067503
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGGCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60354623|gb|DN221596.1|DN221596
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|30088412|gb|CB886617.1|CB886617
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|16926228|gb|BM079296.1|BM079296
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60346808|gb|DN213781.1|DN213781
EST:     CGTTCCTGTTTATGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|28982933|gb|BQ538434.2|BQ538434
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAATAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60398834|gb|DN231650.1|DN231650
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|28985028|gb|BQ539307.2|BQ539307
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60349330|gb|DN216303.1|DN216303
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|50333643|gb|CO528769.1|CO528769
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCCCCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60345394|gb|DN212367.1|DN212367
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60352046|gb|DN219019.1|DN219019
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|149009782|gb|EE041679.2|EE041679
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGC
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGC
EST: gi|211541391|gb|FL468178.1|FL468178
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|149089650|gb|EE178904.2|EE178904
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGC
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGC
EST: gi|211386633|gb|FL468002.1|FL468002
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|211130913|gb|FL136651.1|FL136651
EST:     TGTCATTGCGGTAGTTGATGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: TGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|71327358|gb|DR800292.1|DR800292
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60344730|gb|DN211703.1|DN211703
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|149112850|gb|EE295663.2|EE295663
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|33466593|gb|CF243642.1|CF243642
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCCCCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|211130916|gb|FL136654.1|FL136654
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGGACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|5804633|gb|AI979603.1|AI979603
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
EST: gi|60343169|gb|DN210142.1|DN210142
EST:     CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAG                         ATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT
genomic: CGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCT

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: 218

GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCTCCCGCCATGAACAGGAAGCTGCTGTCCATCGACGCTGCAGGACTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCTCCCGCCATGAACAGGAAGCTGCTGTCCATCGACGCTGCAGGACTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCTCCCGCCATGAACAGGAAGCTGCTGTCCATCGACGCTGCAGGACTCTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgcc ... tttcttgcagATTGTCAACCCGCATAACAAGAACATCAGAGACATTCCGGGCCTAGCACCTCCCGCCATGAACAGGAAGCTGCTGTCCATCGACGCTGCAGGACTCTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGCTACTGACAAATGCATTATGGCGTTCCTGTTTCTGATTGTCTGTGGTGTCATTGCAATAATTGTTGTTAAGgtatgttgccgactctgtgaaggcgtcgtcgtatttattgtgtgcctaaataagattagctatgcttggtgtttagtttaggactagaaaatctctacac

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctagaaaa