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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttacctgctcagtaattttatcgataatacagtttgaatccacatagcactgcatttgtctggatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG

Basic information

species Zea mays
transcript GRMZM2G085960_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085960_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g44370.1 (Oryza sativa), 3'ss of exon 3
--atgttacctgctcagta-attttatcgataatacagtttgaatccacatagcactgcatttgtctggatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG
    |    || |  |  | | |  ||     || || ||  | || ||   || |     || ||||||||| ||   | ||       |  ||| | |||||||||| |||| ||| ||||||| |||||||||||||| |||||| | |||||| ||||||||||||||||| ||  |||||||||||| |||| |||||
gaccgcagacttccgatcatactacatttcctattcaattccagtcaac---gccccatgcttatctggatgagcttgttaatgatgtgctcttgtactttagGGAGGAGAGCCACGTGTTGCTGACTTTGTTCATGGGTCTGATGGCCTGGGGAATTTGTTTCTTCCTGCACCCACTAGTAAGAAGGTTGATGAAAATGCTG

upper sequence: GRMZM2G085960_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA03G35170.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------------atgttacctgctcagtaattttatcgataatacagtttgaatccacatagcactgcatttgt-ctggatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG
                                                                        | |   |  || |  |  |       ||  | |  |||    || |  |      ||| |  |   |||  | ||| || |||   || | | ||  |||| |||||||| ||| |||||||||||||||||||   ||||||  | |||||    || || ||  ||||    | | ||||  ||||| |||||||| 
gtaactattttaatgtgtagatttagcttctctaatgttgattcggtcaatttaggttttaattggatgtgggctttgttttcggctacatccaattgaactcggcctgatctgacttctcctcttttttttgttctctgatattaattat-gatttattttctgcaaaagGGTGGAAAGCCTCGTGTTGCTGATTTTGTTCATGGTAAAGATGGACTAGGGAACACATTCCTACCCCCACCTAAAGGTGAGAAAATTGAGAAAAGTGCTA
















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|74241088|gb|DT649002.1|DT649002
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|32797780|gb|CD950016.1|CD950016
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCNCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|93013944|gb|EB639464.1|EB639464
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCC--GTATTGCTGATTTTGTTCATGGGTCAGATGGCATTG
EST: gi|211348352|gb|FL160894.1|FL160894
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         G-AGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCAT
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCAT
EST: gi|211348356|gb|FL160898.1|FL160898
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|78105353|gb|DV523771.1|DV523771
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|78103961|gb|DV522379.1|DV522379
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|32797544|gb|CD949780.1|CD949780
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|32847882|gb|CD987563.1|CD987563
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGGGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTT
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTT
EST: gi|71448364|gb|DR829414.1|DR829414
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|91048127|gb|EB158545.1|EB158545
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|93017218|gb|EB642738.1|EB642738
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|74238611|gb|DT646525.1|DT646525
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|149058761|gb|EE156779.2|EE156779
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|16925487|gb|BM078555.1|BM078555
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|71432393|gb|DR813443.1|DR813443
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|211348354|gb|FL160896.1|FL160896
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGAT
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGAT
EST: gi|86474150|gb|DY240520.1|DY240520
EST:     CAGGACATCCTGAGGTTCCAATAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|78104295|gb|DV522713.1|DV522713
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|32789762|gb|CD941998.1|CD941998
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
EST: gi|32797907|gb|CD950143.1|CD950143
EST:     CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAG                         GGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG
genomic: CAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGG

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), 47 (downstream exon)
Score: 24

TGTGAGAGAGCAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

TGTGAGAGAGCAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 129

TGTGAGAGAGCAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 38

TGTGAGAGAGCAGGACATCCTGAGGTTCCAGTAGCAGAGGGCAGCCACGAGCCCCTAAAGgttgtttgct ... tgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catagcactgcatttgtctggatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG
                                     atacttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttacctgctcagtaattttatcgataatacagtttgaatccacatagcactgcatttgtctggatgaactgaatgatcgatactttgtgttcattagGGAGGAAAGCCCCGTATTGCTGATTTTGTTCATGGGTCAGATGGCATTGGGAATCTGTTTCTTCCTGCACCCTCTGCTAAGAAGGTTGAGGAAAGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - cctgctc
- - - - - - - - - - - - - - - - - - -tgaatcc
- - - - - - - - - - - - - - - - - - - - - - - - - cactgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg