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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctatgggatatcgccatatcggtttgttttctgcaagtagaacagcattggtattttcttcctcaaatgttgtataactagtgatgatttctttgctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT

Basic information

species Zea mays
transcript GRMZM2G021378_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021378_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g07200.1 (Oryza sativa), 3'ss of exon 4
gtgcgctatgggatatcgccatatcggtttgttttctgcaagtagaacagc--attggtattttc-ttcctcaaatgttgtataactagtgatgatt--tctttgctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT
        |   ||| ||  || | ||||  ||| |||||| | | | |||  || | || || | || ||  ||| ||| || |||| |  |||||  ||||| | |  ||||||| | ||||| ||||||||||||||||||||||| |||||||| | |||||| ||||||||||||||||||||| |  |||| ||||| 
-------gtacaata-cgggattttggttc-tttcctgcaaattggatagcttatggatacttgcgttgcttcaattttgcatcactaatt-tgattcctcttttcaaactgtagAGATTAAAAAGCGCATGGAGAAGGATGTCAATGAGGTGACAAAAACTGCACGTCTGGCAAAATCAAAAGTAGAGAAGTTGAATAAAGAC
















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|78075707|gb|DV504141.1|DV504141
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
EST: gi|40286967|gb|CK327359.1|CK327359
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
EST: gi|76928325|gb|DV171578.1|DV171578
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
EST: gi|38568867|gb|CF974752.1|CF974752
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
EST: gi|76289342|gb|DV028910.1|DV028910
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
EST: gi|71320028|gb|DR796779.1|DR796779
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
EST: gi|78109317|gb|DV527733.1|DV527733
EST:     AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAG                         AGGTNNNNNNNCGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC
genomic: AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCAC

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: 48 (upstream exon), 10 (downstream exon)
Score: 3

AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 194

AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 250

AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 38

AACTCAAATGAGGAGTCAAAAGTTGTCACGAAGGCATCTGCGATGAAAGgtgcgctatg ... ctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattttcttcctcaaatgttgtataactagtgatgatttctttgctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT
                     gtataac  putative branch site (score: 38)
                                     tttctttgctactt  putative PPT
                   ttgtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgctatgggatatcgccatatcggtttgttttctgcaagtagaacagcattggtattttcttcctcaaatgttgtataactagtgatgatttctttgctacttgtagAGGTAAAAAAACGCATGGAGAAGGATGTCAATGAAGTGACAAAGATTGCACGGCTGGCAAAATCAAAAGTAGAGCAACTGAACAAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA