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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgttgttccctgtttatgttcatgttaaactctcaattccaacatgttgtttgttttccag

Basic information

species Zea mays
transcript GRMZM2G124965_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124965_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g08760.2 (Oryza sativa), 5'ss of exon 2
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagct--tctgt-tgttccctg------------tttatgtt-catgttaaactct-caattccaacatgttgtttgttttccag
|| ||| |||||||| ||||||||||||||||||||||| | ||||  |||||| |||||||| || |||||| | |  ||| | ||||||||||||||||| || | |  |   |||  | |  | ||               |  || ||| || ||   |  |||| |||||||||| |||||||  ||
TGATGAATTTCGTCTGAAGTGGGATCCCATGCTTGCATATTTCAAAATTTTGGAGGAGTTCCCCCAAAATGGAACTATGATTATTCACTGGATAAAAAAGgtatgacaacttgacctgcatatctcttgacaagcatatcccccaaattacatattgaatcatgtaatttcaacatgttgcttgttttgtag

upper sequence: GRMZM2G124965_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0020g04870.t01 (Vitis vinifera), 5'ss of exon 3
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgtt--------gttccctgtttatgttcatgttaaactctcaattccaacatgttg--tttgttttccag-----------------------
|| ||| ||| | |  || ||||| || |||||||| || |  |||   ||||| || |||||||| |  |   |||  |||||||||||||||||||||||||||  | | |    |         |   ||  | ||||      | ||  ||   | |||  || |||  ||  | |  ||                        
TGATGAGTTTAGACCTAAATGGGACCCTATGCTTGCTTATTTTAAAATCTTGGAGGAATTCCCTCATACAGCGACAATGATTGTCCACTGGATAAAAAAGgtttgttgaacgtaaaatttgaacacatgtactagtgatgtattgacttaatacttgttcccacaattttgagttgatatctcaactctctgtttattctgtttgcag
















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|5915166|gb|AW052807.1|AW052807
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|149083327|gb|EE172619.2|EE172619
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTTGGGAG-ACGCATAT
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTT-GG-AGGACGCATAT
EST: gi|71769408|gb|DR967345.1|DR967345
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCC-ATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGG
EST: gi|149111705|gb|EE190850.2|EE190850
EST:     TGGATGAGTTCCCTCAGAATGGAGCACCAATTGTCCACTGGATAAAAAAG                         T-CCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGGAGGACGCA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGG-AGGACGCA
EST: gi|91055562|gb|EB165980.1|EB165980
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCA
EST: gi|71437018|gb|DR818068.1|DR818068
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAAATGTCCACTGGATAAAAAAG                         TTCCCATTCTTTTGCAGTGACCGTGAATA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATA
EST: gi|94472323|gb|EB701281.1|EB701281
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAA-G                         TTCCCATTCTTTTGCAGTGACCGTGAATA
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATA
EST: gi|31354728|gb|CD439085.1|CD439085
EST:     TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAG                         TTCCCCATTCTTTTGCAGTGACCGTGAATACAT
genomic: TGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCC-ATTCTTTTGCAGTGACCGTGAATACAT

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), 46 (downstream exon)
Score: 172

TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACAAAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 120

TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACAAAG


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

TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 239

TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccag ... tgttttccagTTCCCATTCTTTTGCAGTGACCGTGAATACATCTTTGGAGGACGCATATGGGAATCTGGGAAGACTTACTATTGTGTTACAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGATTTTCGTCTAAAGTGGGATCCCATGCTTGCATACTCCAAATCTTTGGATGAGTTCCCTCAGAATGGAGCAACAATTGTCCACTGGATAAAAAAGgtttgtccagcttctgttgttccctgtttatgttcatgttaaactctcaattccaacatgttgtttgttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA