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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaacattggtttgaatgttttgtgtttatttttgttttgagttattttggacttttcatatatatttatattatatgctgctgacactacaaa...

Basic information

species Zea mays
transcript AC215244.3_FGT002
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC215244.3_FGT002 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g42690.1 (Oryza sativa), 5'ss of exon 5
TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaacattggtttgaatgttttg--tgtttatttttgttttgagttattttggacttttcatatatatttatattatatgctgctgacactacaaa-
|  || ||||||||||||||| ||||||| |||||||||||||||||   |||| ||||||||||| || |||||||||||||||||||||||||| ||||||| | |  ||  |   | | |  |     |    |||||   ||| |  |   |   |||      | | | | ||   |     | |  |||     |  
TGATTTTGCTGAACCTTCTGGAACTGAAGGAACTGAGGAAGAAGGTGAATATGAAGATGAATCCATTGTCCATCACACTGCCAGTGTTGGTGATGATGAGgtaagggggccagagtgctaagtagtacagctaaggattttaaatttcaaatccctca-actaacggca-agaataatgg-acgaaatacatacatggtcagc

upper sequence: AC215244.3_FGT002 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA04G12950.1 (Glycine max), 5'ss of exon 6
---TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgta----atgagaacattggtttgaatgttttgtgtttatttttgttttgagttattttggacttttcatatatatttatattatatgctgctgacactacaaa
   | | |||||||||  ||||||  | || || ||    |||||    ||  |||| |||||||| || |||||||| ||||| |||||||||||||  |||||     ||   |  |||  | |  |||  |  || |  |   | || |   || |||   |    ||||  || ||||  ||||    ||  |||   |    
AGGTGCCTCTGCTGAAAATTCTGGGGCAGATGAGAC---AGAAGATTTGGGAAATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatatagcactatttttctacatgcat-atgctcttaaatcttctccctt-tttgaaagaaatcatgaat-tttactttatg-attgaagacttgaagtt

upper sequence: AC215244.3_FGT002 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA06G47830.1 (Glycine max), 5'ss of exon 6
---TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgta----atgagaacattggtttgaatgttttgtgtttatttttgttttgagttattttggacttttcatatatatttatattatatgctgctgacactacaaa--
   | | |||||||||  ||||||  | || || ||    |||||    ||  |||| |||||||| || |||||||| ||||| |||||||||||||  |||||     ||   |  |||  | |  |||  |    | || | |  ||| |  || |||   |    ||||    | || || | |||| | |  | |||   ||  
AGGTGCCTCTGCTGAAAATTCTGGGGCAGATGAGACC---GAAGATTTGGGAAATGAAGATGAATCAATTGTTCATCATACTGCTAGTGTTGGTGATGTGGAGgtgtgatatagcactatttttctacatgcatatgctctaatatcttttcg--ttttttgaaagaaatcatg---agttttactctatgat-cgaagacttggaagt

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|61119717|gb|DN560678.1|DN560678
EST:     ATGATGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGA
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGA
EST: gi|60398619|gb|DN231435.1|DN231435
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|78026189|gb|DV494576.1|DV494576
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|20811188|gb|BQ295666.1|BQ295666
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|211020513|gb|FL077077.1|FL077077
EST:     AATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: AATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|60352130|gb|DN219103.1|DN219103
EST:     ATGATGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|148960886|gb|EE011567.2|EE011567
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|60399909|gb|DN232719.1|DN232719
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|149110681|gb|EE190549.2|EE190549
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCA
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCA
EST: gi|71428232|gb|DR809282.1|DR809282
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|20336929|gb|BQ172559.1|BQ172559
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|60401135|gb|DN233942.1|DN233942
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|14245348|gb|BG873930.1|BG873930
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|148986783|gb|EE030579.2|EE030579
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|60355986|gb|DN222959.1|DN222959
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|110958273|gb|EE178325.1|EE178325
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|60341985|gb|DN208958.1|DN208958
EST:     ATGATGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|149096548|gb|EE182297.2|EE182297
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
EST: gi|78115068|gb|DV533456.1|DV533456
EST:     ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAG                         GGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT
genomic: ATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCT

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: 308

TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 493

TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 502

TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 428

TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaa ... catgcaatagGGTCTCAAGAAAGCACTAGATGGTGGAGCCGACAAGGATGAAGAAGACTCTGAGGGAAGAAGGGCCTTACATTTTGCATGTGGGTACGGTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTTCTGCTGAACCTTCTGGTACTGAAGAAACTGAGGAAGAAGGTGGGGATGACGATGAATCCATCGTTCATCACACTGCCAGTGTTGGTGATGAAGAGgtaatgagaacattggtttgaatgttttgtgtttatttttgttttgagttattttggacttttcatatatatttatattatatgctgctgacactacaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA