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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagttctattattggtttcccggctatttattctgtattgttttcttcacccaactctgtgacttgcaattcccag

Basic information

species Zea mays
transcript GRMZM2G408242_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os09g32680.4 (Oryza sativa), 5'ss of exon 7
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagttctatta-----ttggttt---cccggctat--ttattc---tgtattgttttcttcaccca----------actctgtgacttgcaattcccag
 || || ||||| ||| | |||||||| ||||| || || ||| | ||||| |||||||  ||    |||||||||||||||||||||||||||||||| |||||     || ||      ||| | |   || ||||    |  ||    | | ||| | | |||| |||          | | | |      |||||| |||
ACCATATATGATAGCATTAGCCTGCATCTACATTGCAAGCGTTCTTAAAGACAAGGACATAACTCTGTGGTTTGAAGAGCTCCGTGTTGACATGAACATTgtaagtgtgcctgttgatcacttgatcttgccctggctcccatcgtttgattctcttgctattttcatccattaatgattgattgtattttcatcaattctcag

upper sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 8
lower sequence: Vv00s0360g00050.t01 (Vitis vinifera), 5'ss of exon 8
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagc-------agttctattattggtttcccggctatttattctgtattgttttcttcacccaactctgtgacttgcaattcccag------------
|||  |  |||||||  | || ||||||||||| || |||||    |||||||| || ||||| || |||||||||||||| || |||||||||||  | |||||        ||||  | | ||  ||| ||      |  || ||| | ||  |||       |     |    | ||| |    |            
TCCACATCTGATTGCCTTAGCTTGCATATACATTGCAAGTGTACACAAAGATAAAGAAACCACTGCTTGGTTTGAAGAGCTTCGAGTTGACATGAATGTGgtaagtttttttgagttaaaatgttactttgccataacatctttgtgtctcgtcatctatgttacatggacttgggtacaagtattgggtgttgatgtgc

upper sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 8
lower sequence: PP1S18_263V6.1 (Physcomitrella patens), 5'ss of exon 6
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgta------agcagttctattattggtttcccggctatt--tattctgtattgttttcttc-acccaactctgtgacttgcaattc--ccag--------
 |||| |||||||||||| || ||||| ||||| || |||||  | || || |||||||| |   ||||||| |||||||| ||||||||||||||  | |||      |     ||    |  | ||  |  | || |  || | || |  || || |   |   || | ||  | |  |   ||  |  |        
ACCCTTCATGATTGCACTTGCATGCATCTACATCGCCAGTGTGCTCAACGAAAAGGACACAAGGTCATGGTTCGAAGAGCTACGTGTTGACATGAATGTGgtatggtcaaatgtctcccgcagcgtttgtcaagttagtgttagtgtgaacagtattttgagatttaagtgtgccattctctggtcagctggtgtggatg

upper sequence: GRMZM2G408242_T03 (Zea mays), 5'ss of exon 8
lower sequence: PP1S427_18V6.1 (Physcomitrella patens), 5'ss of exon 8
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagttctattattggtttcccggctatttattctgtatt---gttttcttcaccc-aactctgtgacttgcaattcccag------------------------------------------------------------------------------------------------
 || | |||||||||||| || ||||| ||||| || || ||  | ||||| |||||||| |   |||||||||||||||| ||||| ||||||||  | |||    ||   ||     | |   |   ||     |     ||   |||  || ||  | | || |  ||    |  |   |||                                                                                                
ACCTTTCATGATTGCACTTGCATGCATCTACATCGCTAGCGTGCTCAAAGAGAAGGACACAAGGTCATGGTTTGAAGAGCTACGTGTGGACATGAATGTGgta--tggtcgaatgccctgctcagcaattaccatgttcacgttagcgttaactgcattctagctttaagatggtcgttctgcagttagctgttgtggatgtctcttaggggagcttaatttcaaattgtagggctgtgcttgtcatccttttgaacttgtctttgaacttgcacgttcag

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|50333681|gb|CO528807.1|CO528807
EST:     GGTTTGAAGAGCTCCGTGTTGCCATGAACATA                         GTTAAGAATATCTTTATGGAAATATTAGACTTTTATGACCCCTACAAGATT
genomic: GGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|22521611|gb|BU080422.1|BU080422
EST:     ATAAGGACCCCCCAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACCCCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|60352426|gb|DN219399.1|DN219399
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|37373889|gb|CF623269.1|CF623269
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|78022288|gb|DV490675.1|DV490675
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTTTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|32930869|gb|CF035681.1|CF035681
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|78544078|gb|DV621576.1|DV621576
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|60352672|gb|DN219645.1|DN219645
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|60346539|gb|DN213512.1|DN213512
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|5739678|gb|AI947473.1|AI947473
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|22818771|gb|BU498861.1|BU498861
EST:     TAAGGACACCCCAGCATGGTTTGAAGAGCTCCGGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACCCCTACAAGATT
genomic: TAAGGACACCACAGCATGGTTTGAAGAGCTCCG-TGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|71772452|gb|DR970384.1|DR970384
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|74235410|gb|DT643324.1|DT643324
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|211115727|gb|FL229698.1|FL229698
EST:     ATAAG-ACACCACAGCATGGTTTGAAGAGCTCCGTGNTGACATGAACATA                         GGTNAGA-TATCTCTATGGGAGTATTAGACTTCTATGACACCTACA-GAAT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|211507205|gb|FL420316.1|FL420316
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|50333682|gb|CO528808.1|CO528808
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTA
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTA
EST: gi|6742399|gb|AW313214.1|AW313214
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|6760625|gb|AW324724.1|AW324724
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|20301653|gb|BQ164596.1|BQ164596
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|148990759|gb|EE032170.2|EE032170
EST:     TAAGGACACCCCAGCATGGTTTTGA-GAGCTCCGTGTTGACATGAACATA                         A
genomic: TAAGGACACCACAGCATGGTTT-GAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccag-
EST: gi|148990759|gb|EE032170.2|EE032170
EST:     TAAGGACACCCCAGCATGGTTTTGA-GAGCTCCGTGTTGACATGAACATA                         A
genomic: TAAGGACACCACAGCATGGTTT-GAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccag-
EST: gi|148990758|gb|EE032169.2|EE032169
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTTTATGGAAATATTAGACTTTTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|60339571|gb|DN206544.1|DN206544
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTTTATGGAAATATTAGACTTTTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|93282133|gb|EB674397.1|EB674397
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|74235409|gb|DT643323.1|DT643323
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTTTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|211160608|gb|FL453142.1|FL453142
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTGGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTGCAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|18649580|gb|BM498399.1|BM498399
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|71772451|gb|DR970383.1|DR970383
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTTTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|22549285|gb|BU101486.1|BU101486
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATT
EST: gi|148937775|gb|EC881986.2|EC881986
EST:     ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATA                         GTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTAC
genomic: ATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTAC

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), 45 (downstream exon)
Score: 59

TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATTGATCCTCAAAGGGGCATCCCTGAGGATAAGATAAGCCCCGTGATGAACA


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

TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATTGATCCTCAAAGGGGCATCCCTGAGGATAAGATAAGCCCCGTGATGAACA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 52

TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATTGATCCTCAAAGGGGCATCCCTGAGGATAAGATAAGCCCCGTGATGAACA


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

TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagtt ... caattcccagGTTAAGAATATCTCTATGGAAATATTAGACTTCTATGACACCTACAAGATTGATCCTCAAAGGGGCATCCCTGAGGATAAGATAAGCCCCGTGATGAACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCCTACATGATTGCACTGGCCTGCATATACATAGCGAGTGTTTTGAAAGATAAGGACACCACAGCATGGTTTGAAGAGCTCCGTGTTGACATGAACATAgtaagcagttctattattggtttcccggctatttattctgtattgttttcttcacccaactctgtgacttgcaattcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT