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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcag

Basic information

species Zea mays
transcript GRMZM2G009849_T03
intron # 32
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 33
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 50
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcag
||||||||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||| |  || ||| |  |||||| |||| |||| ||| |  |  ||||   |||    | |||    |   ||  |     ||||      
GTTGATATATTTGCTCAGCTTCAGAATGCAAGTGAAGCATTTAGAACCTATATCAGAGATGGGCTAGCTCAGgtttgctatttcaatcctggaggtgtttaagctagttttggtgtttttaactgattggctatta---tcgtttttggctcatgcag-----

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 33
lower sequence: GLYMA10G35140.1 (Glycine max), 5'ss of exon 53
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttg-gtaatctcagttttggaggagtttgagcttgtt---attttaattttgt---ttgaggtacgattgaatttaattacgttgtttgcaatgcag----------------------------
||||| ||||||||||||||||| ||||||||||| |||||| | ||||| || || ||||| || |||||||||| || |  | | || |         ||  |||  |   | ||  |||||||   |  |    ||||||    || |    |||  |      |                              
GTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaatttacttgtattaccacatgttcttaattgaacttgcattttgtatttctaccggcgattgggagtagtagaattgagtatttgaccattggcaattgattttaacattttggcag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 33
lower sequence: GLYMA20G32430.1 (Glycine max), 5'ss of exon 52
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttg-gtaatctcagttttggaggagtttgagcttgtt---atttta-attttgt---ttgaggtacgattgaatttaattacgttgtttgcaatgcag-----------------------------
||||| ||||||||||||||||| ||||||||||| |||||| | ||||| || || ||||| || |||||||||| || |  | | || |         ||  |||  |   |||||  |||||||   |  |    ||||||    || |    |||  |      ||                              
GTTGACATATTTGCTCAGCTTCAAAATGCTAGTGAGGCATTTCGCACCTACATTAGAGATGGTCTTGCTCAGgttgagttaatttacttgtactaacacatgttcttaattggattttgcattttgtatttctaccagcgattgggagtagtagaattgagtatttgacaattggcaattgatttttgacatttttgcag

upper sequence: GRMZM2G009849_T02 (Zea mays), 5'ss of exon 33
lower sequence: Vv00s0652g00030.t01 (Vitis vinifera), 5'ss of exon 22
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatctcagttt-----tggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcag---
|||||||||||||| ||||| || ||||||||||| || ||| | || ||||||||||||||| |||| |||||  | | |   | | |     | ||  | |    | ||   ||     |    ||| |    |  ||   |||  || | |  |||    ||  |   
GTTGATATATTTGCGCAGCTCCAAAATGCTAGTGAGGCGTTTCGGACTTATATCAGGGATGGGTTAGCCCAGgtctgcatttagaatatccaaattgaaaattccaggattacaat--gggtacattttaacaagcagtttcttttcttttcctcctttttgttgttgcag

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|12045716|gb|BF727855.1|BF727855
EST:     AGAATGCTAGTGAAGCATTTAGAACCTATATCAAGGATGGGCTAGCTCAA                         GTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTGC
genomic: AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
EST: gi|211104807|gb|FL044860.1|FL044860
EST:     TATATCAGGGATGGGCTAGCTCAG                         GTGGAGAARAATGCAGCASCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
genomic: TATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
EST: gi|67019308|gb|CO448057.1|CO448057
EST:     AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
genomic: AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
EST: gi|67011174|gb|CO439923.1|CO439923
EST:     AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAG                         GTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC
genomic: AGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCC

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), 48 (downstream exon)
Score: 163

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


Block sizes: 41 (upstream exon), 45 (downstream exon)
Score: 36

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 61

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 122

GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatc ... tgcaatgcagGTGGAGAAGAATGCAGCAGCTGGAAGAACGCCTTCTAGTCTTCCACTGTCCACGCCACCCCCAATAGCAGCAATACCTTCTCCAAAATTGGCACCGTCCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATATATTTGCTCAGCTTCAGAATGCTAGTGAAGCATTTAGAACCTATATCAGGGATGGGCTAGCTCAGgttggtaatctcagttttggaggagtttgagcttgttattttaattttgtttgaggtacgattgaatttaattacgttgtttgcaatgcag

- - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA