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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgtctccagataaaattatcttccatagttccattataagatttacatgtcaactctaaccgcctatgttttcttcatttaaaaaaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC

Basic information

species Zea mays
transcript GRMZM2G159285_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G159285_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g53150.1 (Oryza sativa), 3'ss of exon 4
gttagtgtctccagataaaattatcttccatagttccattataagatttacatgtcaactctaaccgcctatgttttcttcatttaaaaaaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC-
|| ||| ||| ||| |||||||  ||| | |           |||||||| || | || ||  ||| | | ||| |      |||         | ||||||||||| | |||||||||| |||||||| |||||||| | | | |||  |||| || ||||  | | ||| || ||||||||||  |||||||||||  
gtcagtatcttcagctaaaatttgctttcgtgtc--------aagatttatatcttaattcacaccccttgtgtgtgtggtttttct-------tccagCACCAAGAGCAAAGGACAAGTACAAGAACAAGAGCTGAAAATGTTGCAGTATTAA-GATGCTGAGCATGGTGCCATAAGAATGGTGTTCTTGCAGTGTGTT
















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|50339634|gb|CO534760.1|CO534760
EST:     CTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: CTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|37384582|gb|CF629379.1|CF629379
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|71757626|gb|DR955563.1|DR955563
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|37381992|gb|CF627908.1|CF627908
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|20208504|gb|BQ134593.1|BQ134593
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|28982929|gb|BQ538419.2|BQ538419
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|5871753|gb|AW018224.1|AW018224
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATGCAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|37381948|gb|CF627882.1|CF627882
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTTAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|8576974|gb|BE129611.1|BE129611
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|12047139|gb|BF729278.1|BF729278
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|71771347|gb|DR969284.1|DR969284
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CCCCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|71760459|gb|DR958396.1|DR958396
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|6056635|gb|AW091040.1|AW091040
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|91054479|gb|EB164897.1|EB164897
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|78544346|gb|DV621844.1|DV621844
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|14203793|gb|BG837470.1|BG837470
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|18180907|gb|BM382117.1|BM382117
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|18181502|gb|BM382712.1|BM382712
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|89755014|gb|DY685590.1|DY685590
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAGGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|76020197|gb|DT947367.1|DT947367
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|78108965|gb|DV527382.1|DV527382
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|78119357|gb|DV537741.1|DV537741
EST:     GTCATGCAGGCGTTTGAGGATCATGAAGAGCTTTGAAGCCATAGGTCTTG                         CCCCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|76285970|gb|DV025538.1|DV025538
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|37398188|gb|CF636404.1|CF636404
EST:     AGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: AGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|78180321|gb|DV550694.1|DV550694
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGTTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAACAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
EST: gi|18181098|gb|BM382308.1|BM382308
EST:     GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTG                         CACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG
genomic: GTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCG

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: 44

GATGTTTGTCGAGTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 215

GATGTTTGTCGAGTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 75

GATGTTTGTCGAGTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 48

GATGTTTGTCGAGTCATGCAGGCGTCTGAGGATCATGAAGAGCTCTGAAGCCATAGGTCTTGgttagtgtct ... aaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttacatgtcaactctaaccgcctatgttttcttcatttaaaaaaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC
              ctctaac  putative branch site (score: 48)
                         tatgttttcttcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgtctccagataaaattatcttccatagttccattataagatttacatgtcaactctaaccgcctatgttttcttcatttaaaaaaaaatacagCACCAAGAACGAAGGACAAGTGCAAGAACAGGAGCTGAAGAAGATACAGCGTTAAAGACGCTGCCCGTTGTGTCAAAAGAATGGTGCCCTTGCAGTGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA