Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctctgctctgatacggcacttttttagcatcaagggctgctacatgtgaaccttgccatcctttagttgcttgtttagtgccttgcgactgcga...

Basic information

species Zea mays
transcript AC230013.2_FGT007
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC230013.2_FGT007 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g47660.1 (Oryza sativa), 5'ss of exon 3
GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctctgctctgatacggcacttttttagcatcaagggctgct--acatgtg-aaccttg--ccatcctttagttgc-ttgtttagtgccttgcgactgcga
|||||||||||||||| |||||||||| |||||||||||||| ||| | || |||||||||||||||   ||      | | |||     | ||| ||    |  ||| |   |||| || ||||| |  | |    ||| |     || ||     ||    | ||   
GTACTTCCTGAGGAAGCTGAAGAAGGTGAAGAAGAGCAACGGCCAGATGCTCGCCATCAACGAGgta---ctagaaattcaaacgtattgtatttcgccctgattgctccctgacatttgtaacctagttctagatattaatcatactgattgaccgctaataagtg---
















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|5688510|gb|AI941525.1|AI941525
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|5932717|gb|AW057078.1|AW057078
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|15100313|gb|BI396104.1|BI396104
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211263956|gb|FL049653.1|FL049653
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTATGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|18384240|gb|BM417439.1|BM417439
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211268823|gb|FL049675.1|FL049675
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTATGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|29130285|gb|CB380989.1|CB380989
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|5343072|gb|AI795482.1|AI795482
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|31405721|gb|CD484453.1|CD484453
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211261521|gb|FL049637.1|FL049637
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTATGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|29544754|gb|CB605362.1|CB605362
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211261516|gb|FL049632.1|FL049632
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTATGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|9794359|gb|BE552667.1|BE552667
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|5398753|gb|AI812218.1|AI812218
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211259082|gb|FL049626.1|FL049626
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|89757074|gb|DY686828.1|DY686828
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|18383730|gb|BM416930.1|BM416930
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|31358983|gb|CD443340.1|CD443340
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|20301341|gb|BQ164284.1|BQ164284
EST:     AGTTGAAGAAGGTTAATAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|15313528|gb|BI478745.1|BI478745
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211268834|gb|FL049686.1|FL049686
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTATGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|211263947|gb|FL049644.1|FL049644
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|29130286|gb|CB380990.1|CB380990
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|87153228|gb|DY398017.1|DY398017
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|22542281|gb|BU092719.1|BU092719
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
EST: gi|18649600|gb|BM498419.1|BM498419
EST:     AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAG                         ATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC
genomic: AGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGC

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: 1222

GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGCTACCAGAGCAGAACCGGCTACCACAACATGTACAAGGAGTACCGCGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 887

GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGCTACCAGAGCAGAACCGGCTACCACAACATGTACAAGGAGTACCGCGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 863

GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGCTACCAGAGCAGAACCGGCTACCACAACATGTACAAGGAGTACCGCGACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 397

GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctct ... gatgtggcagATCTTCGAGCGTAACCCGACGACGATCAAGAACTACGGCATCTGGCTGCGCTACCAGAGCAGAACCGGCTACCACAACATGTACAAGGAGTACCGCGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCCTGAGGAAGTTGAAGAAGGTTAAGAAGAGCAACGGTCAGGTCCTGGCCATCAACGAGgtatgtctctgctctgatacggcacttttttagcatcaagggctgctacatgtgaaccttgccatcctttagttgcttgtttagtgccttgcgactgcga

- - - - - - - - TTGAAG
- - - - - - - -  TGAAGA
- - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - AGAGCA