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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcctgggtgggttaacttgtatgacaattattaattctctttgaatttaggttaatgaatctcgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT

Basic information

species Zea mays
transcript GRMZM2G147671_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147671_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 4
gtaggcctgggtgggttaacttgtatgacaattattaattctctttgaatttaggttaatgaatctcgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT
          ||  | |||||||||||  |  |     || | | ||| |   |||| ||||  || | |   | | |||| |||||||| |||||||||||| ||||||| ||||||||||| |||||||| ||||| ||||| ||||||||||| ||||||||||||||| | ||||||
----------gtatgataacttgtatggtacct-----ttttatatgagtcgcggttgatgatgctggcctaatctttcagCCCTGTGAAATACGACAAGAAAGTTTTGGAAACAATCGGGAAAAAGCTGAAGAAGAATAATGTGGCTCTTGACATCGTTGACTTTGGTGAAACCGATGAT
















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|211069192|gb|FL190617.1|FL190617
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|9254597|gb|BE345080.1|BE345080
EST:     CGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211071930|gb|FL190632.1|FL190632
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|31353854|gb|CD438211.1|CD438211
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|60350002|gb|DN216975.1|DN216975
EST:     GCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: GCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069191|gb|FL190616.1|FL190616
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211071927|gb|FL190629.1|FL190629
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|29947654|gb|CB816768.1|CB816768
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069188|gb|FL190613.1|FL190613
EST:     ATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTTCATCGGAAG                         TCCTGTGAAGTACGACNAGAAAATTTTGGAGACNATCGGGAAGAAGCTGAA
genomic: ATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATT-CATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|5343122|gb|AI795532.1|AI795532
EST:     TCGCCAGAACAAGAGGCAGCAGCAGGAGGATTATAGCATTCATCGGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGG
genomic: TCGCCAGAACAAGAGGCAGCAGCAG-AGGATTATAGCATTCATCGG-AAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGG
EST: gi|211066454|gb|FL190609.1|FL190609
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|67041049|gb|CO467304.1|CO467304
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211047092|gb|FL234544.1|FL234544
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|47961624|gb|CN844333.1|CN844333
EST:     CATCGCCAGAACAAGAGGCGGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|9824997|gb|BE575199.1|BE575199
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069189|gb|FL190614.1|FL190614
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069199|gb|FL190624.1|FL190624
EST:     CATCGCCAGAATAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAGTTTTG
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTG
EST: gi|22472983|gb|BU037463.1|BU037463
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGA
EST: gi|211069196|gb|FL190621.1|FL190621
EST:     CATCGCCAGAATAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAA
EST: gi|67030433|gb|CO459182.1|CO459182
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|32915709|gb|CF020521.1|CF020521
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069190|gb|FL190615.1|FL190615
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|31360558|gb|CD444915.1|CD444915
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|9952492|gb|BE639075.1|BE639075
EST:     AGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: AGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069198|gb|FL190623.1|FL190623
EST:     ATCGCCAGAATAAGAGGCAGCAGCAGAAGATTATAGCATTCATCGGGAAG                         TCCTGTGAAGTACGAACAAGAAAGTTTT
genomic: ATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGG-AAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGA-CAAGAAAATTTT
EST: gi|211069194|gb|FL190619.1|FL190619
EST:     ATCGCCAGAACAAGAGGCAGCAGCAGAGGATTYATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGANAATCGGGAAGAAGCTGAA
genomic: ATCGCCAGAACAAGAGGCAGCAGCAGAGGATT-ATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
EST: gi|211069200|gb|FL190625.1|FL190625
EST:     CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAG                         TCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA
genomic: CATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAA

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), 49 (downstream exon)
Score: 689

CTGAGGCAAACTTGGCTGCGGCAATCCAGGTTGCTCAGCTTGCGCTAAAGCATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 538

CTGAGGCAAACTTGGCTGCGGCAATCCAGGTTGCTCAGCTTGCGCTAAAGCATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 321

CTGAGGCAAACTTGGCTGCGGCAATCCAGGTTGCTCAGCTTGCGCTAAAGCATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 483

CTGAGGCAAACTTGGCTGCGGCAATCCAGGTTGCTCAGCTTGCGCTAAAGCATCGCCAGAACAAGAGGCAGCAGCAGAGGATTATAGCATTCATCGGAAGgtaggcctgg ... tgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacaattattaattctctttgaatttaggttaatgaatctcgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT
     ttattaattctctttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcctgggtgggttaacttgtatgacaattattaattctctttgaatttaggttaatgaatctcgtcatgtgtatcagTCCTGTGAAGTACGACAAGAAAATTTTGGAGACAATCGGGAAGAAGCTGAAAAAGAACAATGTTGCTCTTGACATTGTTGACTTTGGTGAATCTGATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC