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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgccataaatatgtgccggatatttgtatttttctattcttgctgagcaatttaccatatgtctcattag

Basic information

species Zea mays
transcript GRMZM2G120302_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120302_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os06g11180.1 (Oryza sativa), 5'ss of exon 14
GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgccataaatatgtgccggatatttgtatttttctattcttgctgagcaatttaccatatgtctcattag----------------------------
||  |||||||||||||||||  ||||||||||||| |||||||| ||||||||||| |||||||| ||||| |||||||||||||||||| | |||||||||||||   ||| || | |   ||||  |  | ||||    ||| |    |   |  || || |   |  ||  |                            
GCGACGCCTTTGTATTACTGGGCGATCAGCAGGTGGGTACACTACGTTAGCTTCACTCGCATTCAGGGACACATTCAAGGCTGGAGCTTCTTTGTATGGTgtaagtt---atatatctttctaggattctgcttttttggctttcctataaatgtacataacaaagaaca-atgggggctgcaggttctagatttcttgtgatt

upper sequence: GRMZM2G120302_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv18s0001g11150.t01 (Vitis vinifera), 5'ss of exon 14
GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttg----------ccataa------atatgtgccggatatttgtatttttctattcttgctgagcaatttaccatatgtctca--ttag------
  | ||||| ||    |||||| | ||||| ||||||| ||| || |||||| | ||||| |||| ||| |  |||||||||||||||||  | ||||||||||||||          ||| ||       ||| |||  ||  | | |  || | |  || | |  ||||  | |    |  ||||   |||       
AAAACGCCTATGCGCAACTGGTGGTTCAGCTGGTGGATTCACAACATTAGCTGCTCTTGCTTTCAAAGAAATTTTCAAGGCTGGAGCTTCCTTGTATGGTgtaagttgttcgatcctcccacaatatgaggtatttgctagaggtatttggttgtttcatccttcaaagcagctgatttgacatctccacttaaaagact

upper sequence: GRMZM2G120302_T02 (Zea mays), 5'ss of exon 14
lower sequence: Vv18s0001g11140.t01 (Vitis vinifera), 5'ss of exon 14
GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagtt----gccataaatatgtgccggatatttgtatttttctattctt--gctgagcaatttaccatatgtctcattag------------------
  | || || || || |||||  | || || |||||||| || || |||||| | ||||| |||||||| |||||||| |||||||||||  | |||||||| ||||      |       | |  | ||||  | |  || ||   ||||   |  ||    ||   |||| ||    ||                   
TGATCGACTCTGCATAACTGGGGGCTCTGCTGGTGGATATACAACATTAGCTGCTCTTGCTTTCAGAGAAACGTTCAAAGCTGGAGCTTCCTTGTATGGTgtgagttcttgatcgagcgattttttcagatacatttggttgtcctgtctttaacacagttgatttggatatctccacctaaaataactaagaaactgtc

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|33091583|gb|CF051577.1|CF051577
EST:     CGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|5847476|gb|AW000555.1|AW000555
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACACACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|6031233|gb|AW076135.1|AW076135
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GGTGGGGACTTGACTCTGTTGAGAGCGGAGACACACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|148972938|gb|EE023964.2|EE023964
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|148961815|gb|EE012596.2|EE012596
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|32935186|gb|CF039998.1|CF039998
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|32934798|gb|CF039610.1|CF039610
EST:     CGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|211313026|gb|FL032573.1|FL032573
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|148964887|gb|EE015749.2|EE015749
EST:     CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
genomic: CTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT
EST: gi|78023231|gb|DV491618.1|DV491618
EST:     ACACGTTCAAGGCTGGAGCTTCTCTCTATGGT                         GTTGGGGACTTGACTCTGTTGAGAGCGGAGACACACAAATTTGAGTCTCAT
genomic: ACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCAT

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: 156

GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 123

GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 119

GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 101

GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgcc ... gtctcattagGTTGGGGACTTGACTCTGTTGAGAGCGGAGACGCACAAATTTGAGTCTCATTATATGGACAATCTTGTAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCGCCTTTGTATTACTGGTAGATCAGCAGGTGGATACACTACTTTAGCTTCACTTGCATTCAGAGACACGTTCAAGGCTGGAGCTTCTCTCTATGGTgtaagttgccataaatatgtgccggatatttgtatttttctattcttgctgagcaatttaccatatgtctcattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT