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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatgaagtatacgtgttactttctgtttcatatgatggctaaccaatccgatatgttcccatagcatctgcatggacttatgtaaagcctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC

Basic information

species Zea mays
transcript GRMZM2G376727_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g01307.1 (Oryza sativa), 3'ss of exon 1
-----ttgcatgaagtatacgtgttactttct--gtttcatatgatggctaaccaatccgatatgttcccatagcatctgcatggacttat-gtaaagcctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
     |   ||   | ||  || |||||||||   | | |||||||||| || |||     ||| | | ||||| |     ||  ||| |  |||||   |||||||| |||||||||||||||    ||||||| ||  |||||||||   | ||||||||||||||| |||||||||  || |||||||||||||||||||||||
tcttttcctattttggattagt-ttactttctctatgtgatatgatggc-aagcaactatgtatat-cacatagta-----ataaactgaccgtaaaatttattgcagAACTGCCTATGATGTGAGCATTAATGATGATACTTGGCCAAAGGAGGCATTTGAGCTTGTCTCTGGAGAGATGTCAAAGACATTGGAAAGGCTTGACCC

upper sequence: GRMZM2G376727_T05 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g01307.2 (Oryza sativa), 3'ss of exon 1
ttgcatgaagtatacgtgttactttctgtttcatatgatggctaaccaatccgatatgttcccatagcatctgcatggacttat-gtaaagcctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
                                                                          ||  ||| |  |||||   |||||||| |||||||||||||||    ||||||| ||  |||||||||   | ||||||||||||||| |||||||||  || |||||||||||||||||||||||
-----------------------------------------------------------------------gtaataaactgaccgtaaaatttattgcagaactgcctatgatgtgagcattaatgatgatacttggccaaaggaggcatttgagcttgtctctggagagATGTCAAAGACATTGGAAAGGCTTGACCC
















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|15590113|gb|BI674729.1|BI674729
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|9255123|gb|BE345591.1|BE345591
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGATCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|60347158|gb|DN214131.1|DN214131
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|78080233|gb|DV508645.1|DV508645
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|149106143|gb|EE291820.2|EE291820
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|60355754|gb|DN222727.1|DN222727
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|30706031|gb|CD059006.1|CD059006
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|78107599|gb|DV526017.1|DV526017
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|60354184|gb|DN221157.1|DN221157
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|211379488|gb|FL165247.1|FL165247
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|21987232|gb|BQ778760.1|BQ778760
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|211354951|gb|FL243591.1|FL243591
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|74243940|gb|DT651854.1|DT651854
EST:     GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: GGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|16919381|gb|BM074163.1|BM074163
EST:     CCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: CCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|24765720|gb|CA400879.1|CA400879
EST:     ACAACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: ACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
EST: gi|211130311|gb|FL066378.1|FL066378
EST:     AACCAGGGATCCGC                         GACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT
genomic: AACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATT

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: 238

CGCCCTTTGTCGTCGCGCACAAGAAGGTTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 247

CGCCCTTTGTCGTCGCGCACAAGAAGGTTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 251

CGCCCTTTGTCGTCGCGCACAAGAAGGTTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 264

CGCCCTTTGTCGTCGCGCACAAGAAGGTTTCGCTCTCCCGCCCCAAGCCGGGCGTCGAGCGCGTCGCCGTCTCCCTCGACCTCTACAACCAGGGATCCGCgtgagtaccg ... cctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatccgatatgttcccatagcatctgcatggacttatgtaaagcctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC
                                   ttatgtaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatgaagtatacgtgttactttctgtttcatatgatggctaaccaatccgatatgttcccatagcatctgcatggacttatgtaaagcctattgcagGACTGCCTATGATGTGTCACTTAATGACGACTCTTGGCCAACACAAGCATTTGAGCTTGTCACTGGAGAGAAATCGAAGACATTGGAAAGGCTTGACCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
-tgcatga
- - - - - - - - tgttact
- - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - -tatgatg
- - - - - - - - - - - - - - - - - - - - -ctaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgg