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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttattctttgtagatatgagtatctaaaaatctaggctagtcatgcatttcttgtgctttctgtattcatgatgtcactggtcccatgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG

Basic information

species Zea mays
transcript GRMZM2G028004_T05
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028004_T05 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g27850.1 (Oryza sativa), 3'ss of exon 5
atatttattctttgtagatatgagtatctaaaaatctaggctagtcatgcatttcttgtgctttctgtattcatgatgtcactggtcc--catgttctct-----agGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG
 |   | || ||||||| | |   | ||| |||  |  |       ||   |||| ||| ||||   ||||   | | |  ||       ||| || | |     ||||||| |||||| |||| || || ||||||||||||||||||| ||||||||||||||| |  |||||| |||||
-tgggt-ttttttgtagttctctatttctgaaaccccggaa-----atatttttcatgtccttttaatatttcggttattgctaacttggcatattttgtggaacagGGTGTTAAAAGTAATGTCCGTACAAGTTCTGGTATGTTTGTGAGTTCTGAAGAAAGAAAGTTACCAGTCATTCAG
















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|24768774|gb|CA403903.1|CA403903
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|37395929|gb|CF635251.1|CF635251
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|31353632|gb|CD437989.1|CD437989
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|60357917|gb|DN224890.1|DN224890
EST:     AGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: AGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|31364418|gb|CD448773.1|CD448773
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTCCTGGTATGTTGGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|24768702|gb|CA403831.1|CA403831
EST:     TGTAGTGGATG-TGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: TGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|67013389|gb|CO442138.1|CO442138
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|5901353|gb|AW042453.1|AW042453
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|67013387|gb|CO442136.1|CO442136
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|31364601|gb|CD448956.1|CD448956
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|211001688|gb|FL223536.1|FL223536
EST:     CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: CTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
EST: gi|60355576|gb|DN222549.1|DN222549
EST:     TAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAG                         GGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA
genomic: TAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAA

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: 79

GAGTGTGATTACCTAATGGCAATTGCTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 54

GAGTGTGATTACCTAATGGCAATTGCTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG


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

GAGTGTGATTACCTAATGGCAATTGCTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 48

GAGTGTGATTACCTAATGGCAATTGCTAGACCAAGACTCCAAATATCCACTGTAGTGGATGTTGCAACAGGAAAGgtatgttggt ... tgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcatttcttgtgctttctgtattcatgatgtcactggtcccatgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG
                                             tgttctct  CT-rich tract
     atttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttattctttgtagatatgagtatctaaaaatctaggctagtcatgcatttcttgtgctttctgtattcatgatgtcactggtcccatgttctctagGGTGTAAAAAGTGATGTTCGGACGAGTTCTGGTATGTTTGTGAATTCTGAAGAAAGAAAATCTCCAGTCGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggtcc