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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGCAGCTTCTTCTTCTTGTACGCCTCACGCAGCGCCGACTTCTGCTTCTGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtggaaaccacggatccacgattaagttaagtccgaagcaaagccagtttgataaaagaggaacaagggcgagcgccgtcaacgcacat

Basic information

species Zea mays
transcript GRMZM5G805725_T01
intron # 2
splice site 5'
intron type U2

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|211414434|gb|FL217540.1|FL217540
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211021165|gb|FL217567.1|FL217567
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|33103906|gb|CF063866.1|CF063866
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|31405885|gb|CD484617.1|CD484617
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211416981|gb|FL217550.1|FL217550
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211026053|gb|FL217603.1|FL217603
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACABCCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211416983|gb|FL217552.1|FL217552
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211026058|gb|FL217608.1|FL217608
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|32914141|gb|CF018953.1|CF018953
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGAGTAGCAA
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211023600|gb|FL217588.1|FL217588
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGS-TACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211411888|gb|FL217529.1|FL217529
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
EST: gi|211411880|gb|FL217521.1|FL217521
EST:     TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGAT                         CTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG
genomic: TGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAG

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 1 RNA-Seqlibrary.


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 6

GGAGCAGCTTCTTCTTCTTGTACGCCTCACGCAGCGCCGACTTCTGCTTCTGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtgg ... caacgcacatCTTGGAGAGCTTGTTGGGAGCCCCGCCGGTGACCTTGGCTACGCGTAGCAGGGAGAGCTCCGACTTAAACTCCTTAAGCTGCGCTTGCAGATCCGCCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGCAGCTTCTTCTTCTTGTACGCCTCACGCAGCGCCGACTTCTGCTTCTGCGAGATGACGGTCAGCACGCGCGCGATGGAGGTGCGCACAACCTTGCTgcaagagtggaaaccacggatccacgattaagttaagtccgaagcaaagccagtttgataaaagaggaacaagggcgagcgccgtcaacgcacat

- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG