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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctctgctgactactggcagacccagtgcccgggaaagggataaactgaggcaagcctttcccccgcaaatatggagagctgcttcgaacctgtg...

Basic information

species Zea mays
transcript GRMZM2G144730_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 2
TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctctgctgactac-tggcagacccagtgcccgggaaagggataaactgaggcaagcctttcccccgcaaatatggagagctgcttcgaacctgtg
||||||||||||||| ||||||||||| ||  ||||||| ||||||||||||||  |||| |||||||| ||||| ||||| || |||||||| || ||||||||   | | |||  || ||  |     | |||    | ||   || | ||| |   |    |    |  ||   ||| ||                  
TGGTGACCACCAGTCGCACCAGAAGGTGATTGATTTGGTGAAGGAGTACAATGCGAAGAATACTGATGGCAATGTCATTGCTATTATGCTGGATACCAAGgtatactgccgttgaacacatgaaattttgaatgctgcagcaa---atgagctgtgatga----tcgaacttcagtgatgcag------------------
















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|148966755|gb|EE017835.2|EE017835
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
EST: gi|88749445|gb|DY533586.1|DY533586
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
EST: gi|148981227|gb|EE027511.2|EE027511
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
EST: gi|148928929|gb|EC873987.2|EC873987
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
EST: gi|149048881|gb|EE048381.2|EE048381
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
EST: gi|78075400|gb|DV503834.1|DV503834
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
EST: gi|148958744|gb|EC905021.2|EC905021
EST:     ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAG                         GGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA
genomic: ATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAA

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: 130

TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAAGGGCAAGAGTTCAATTTCACAATTAAAAGAGGGGTGAGCACTGAAGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAAGGGCAAGAGTTCAATTTCACAATTAAAAGAGGGGTGAGCACTGAAGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAAGGGCAAGAGTTCAATTTCACAATTAAAAGAGGGGTGAGCACTGAAGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 116

TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctct ... atggatgcagGGTCCTGAAGTTAGAAGTGGGGATGTTCCAGAGCCAATTATGCTCAGTGAAGGGCAAGAGTTCAATTTCACAATTAAAAGAGGGGTGAGCACTGAAGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGACCACCAGTCACACCAGAAGGTTATCAATTTGGTCAAGGAGTACAATGCACAGAACACTGATGGAAATGTTATTGCCATCATGCTGGACACTAAGgtatatctctgctgactactggcagacccagtgcccgggaaagggataaactgaggcaagcctttcccccgcaaatatggagagctgcttcgaacctgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccgc