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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttagttcaacttgactgtactgggtaccactatgttgtcagctagttgatggaggacaaatgtgagttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC

Basic information

species Zea mays
transcript GRMZM2G074373_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G074373_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os12g13170.1 (Oryza sativa), 3'ss of exon 11
gtaattgttagttcaacttga-ctgtactgggtaccactatgttgt------cagctagttgatggaggacaaatgtgagttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC
||| ||||| || ||  |  | || |||||| ||  | ||| || |      |    | |||||| ||   || | | | || ||||||||||||||||||||||||||||||||||||| ||||||||||| |||||| ||||||||||||||||||| ||||| |||||||| |||||||| || |
gtatttgtttgtgcatttcaagctatactggatagaattatcttttgtagtgccttcaattgatgaagcctaact-taaattctgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGAAGTTTTAAAGCAAGAAAATACTTCACTTAGAGATGAAGTGAACCGGATCAGAAAGGAGTATGATGAGC
















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|78090596|gb|DV518970.1|DV518970
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|94479027|gb|EB707985.1|EB707985
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|31358760|gb|CD443117.1|CD443117
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|149110852|gb|EE294350.2|EE294350
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|211028676|gb|FL452179.1|FL452179
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|211028675|gb|FL452178.1|FL452178
EST:     AATAGGGAGTCTGCACGCAAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: AATAGGGAGTCTGCACGC-AGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|71318159|gb|DR795842.1|DR795842
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|60345262|gb|DN212235.1|DN212235
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|60399438|gb|DN232250.1|DN232250
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|89251780|gb|DY623566.1|DY623566
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGGGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|110190661|gb|EC872559.1|EC872559
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|40485763|gb|CK394726.1|CK394726
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
EST: gi|24766396|gb|CA401550.1|CA401550
EST:     GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAG                         GCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT
genomic: GAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAAT

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), 47 (downstream exon)
Score: 70

GATGAACGTGAACTCAAAAGGCAAAAAAGAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 73

GATGAACGTGAACTCAAAAGGCAAAAAAGAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

GATGAACGTGAACTCAAAAGGCAAAAAAGAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 104

GATGAACGTGAACTCAAAAGGCAAAAAAGAAAACAGTCTAATAGGGAGTCTGCACGCAGATCTAGGTTGCGTAAACAGgtaattgtta ... agttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgggtaccactatgttgtcagctagttgatggaggacaaatgtgagttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC
                        agttgat  putative branch site (score: 104)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttagttcaacttgactgtactgggtaccactatgttgtcagctagttgatggaggacaaatgtgagttttgcagGCTGAATGTGAGGAGTTGGCTCAACGTGCTGATGTTTTAAAGCAGGAAAATGCTTCACTTAGAGATGAAGTAAACCGTATCAGAAAAGAGTATGAGGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG