Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcccttggagtgggtgccctgttcatgggcaccggctgcacgtgccctcgctcgagcctggtgatttatgtgttttaaagttttcttttctaaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA

Basic information

species Zea mays
transcript GRMZM2G114172_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 1
--gcccttggagtgggtgccctgttcatgggcaccggctgcacgtgccctcgctcgagcctggtgatttatgtgttttaaagttttcttttctaaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA
      ||    | |      ||    ||  ||||   | |   || || |  | ||   || |  | ||| |  |||  | |  | || | ||  |||||| ||  ||||||| ||||||||||| | ||||||||||||||| ||| ||||  | |||| |||  | |  |||||||||| |||  | || |||||||||
taatggttctgtttgaaaatttgaatttgtacaccatgtacttatgtcc-catttgaaggtgctt-tctatttactttgcattaattttgtatatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACTCAATGATTATGAAATAGGCCAGAATGAAGTTACTGCTATCAAGGATAAA
















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|211146533|gb|FL321961.1|FL321961
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|78113538|gb|DV531929.1|DV531929
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|116813073|gb|EC855467.1|EC855467
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACTATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|211460046|gb|FL333662.1|FL333662
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTT
EST: gi|78106134|gb|DV524552.1|DV524552
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|71428299|gb|DR809349.1|DR809349
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|211361683|gb|FL316886.1|FL316886
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTTGTCGGCCAAGAAGATGATCCGGAGTTAC
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTT-GTCGGCCAAGAAGATGATCCGGAGTTAC
EST: gi|6022603|gb|AW067415.1|AW067415
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACTATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|78090561|gb|DV518935.1|DV518935
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|148958197|gb|EC904402.2|EC904402
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|101394403|gb|EB819136.1|EB819136
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|31405818|gb|CD484550.1|CD484550
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|76021044|gb|DT948214.1|DT948214
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|211472060|gb|FL313866.1|FL313866
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGG-AAGATCAGCATGATCGG                         TACAATTKAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|149088593|gb|EE177708.2|EE177708
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|211318594|gb|FL124207.1|FL124207
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|211164210|gb|FL365736.1|FL365736
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
EST: gi|211227127|gb|FL350907.1|FL350907
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAG
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAG
EST: gi|71772417|gb|DR970350.1|DR970350
EST:     CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGG                         TACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT
genomic: CTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACT

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: 47 (upstream exon), 47 (downstream exon)
Score: 126

AGACGCTACTCTACCCCAAGCTCATACTTAAGGACATGGACGACTCCACCCTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 78

AGACGCTACTCTACCCCAAGCTCATACTTAAGGACATGGACGACTCCACCCTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 94

AGACGCTACTCTACCCCAAGCTCATACTTAAGGACATGGACGACTCCACCCTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

AGACGCTACTCTACCCCAAGCTCATACTTAAGGACATGGACGACTCCACCCTCCTCTCCTCCATCCCTTTCAAGCCCAACGGGAAGATCAGCATGATCGGgtaagcggga ... taaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcgctcgagcctggtgatttatgtgttttaaagttttcttttctaaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA
                                          ttctaaa  putative branch site (score: 164)
                                   ttttcttttct  CT-rich tract
                  atttatgtgttttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcccttggagtgggtgccctgttcatgggcaccggctgcacgtgccctcgctcgagcctggtgatttatgtgttttaaagttttcttttctaaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - ggtgccc
- - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - cggctgc
- - - - - - - - - - - - - - - - - - - - - tgccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cctggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttt