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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttggattaaccaagtgtttcttcagtcggtcggtcgattggtgagcccaaactctggtgtcctgatgttcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA

Basic information

species Zea mays
transcript GRMZM2G132060_T01
intron # 2
splice site 3'
intron type U2

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|211162505|gb|FL243924.1|FL243924
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAATAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211162502|gb|FL243921.1|FL243921
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211160898|gb|FL243904.1|FL243904
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAATAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211164093|gb|FL243928.1|FL243928
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|23357746|gb|BU645395.1|BU645395
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|20811117|gb|BQ295595.1|BQ295595
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211159306|gb|FL243892.1|FL243892
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211160905|gb|FL243911.1|FL243911
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAATAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148930320|gb|EE284721.2|EE284721
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148936928|gb|EC881083.2|EC881083
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148974670|gb|EE025472.2|EE025472
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|31359279|gb|CD443636.1|CD443636
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211164092|gb|FL243927.1|FL243927
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAATAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211162500|gb|FL243919.1|FL243919
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGC
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGC
EST: gi|211159299|gb|FL243885.1|FL243885
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148944299|gb|EC889396.2|EC889396
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|32929819|gb|CF034631.1|CF034631
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211160895|gb|FL243901.1|FL243901
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAATAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|5566945|gb|AI881856.1|AI881856
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGG
EST: gi|21987171|gb|BQ778699.1|BQ778699
EST:     ATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: ATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148931686|gb|EC874876.2|EC874876
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211159308|gb|FL243894.1|FL243894
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|5555529|gb|AI881480.1|AI881480
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|50336536|gb|CO531662.1|CO531662
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|91050200|gb|EB160618.1|EB160618
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211162494|gb|FL243913.1|FL243913
EST:     NCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211162496|gb|FL243915.1|FL243915
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAATAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|87155460|gb|DY400249.1|DY400249
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211159303|gb|FL243889.1|FL243889
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211159301|gb|FL243887.1|FL243887
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148931684|gb|EC874873.2|EC874873
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|148966452|gb|EE017460.2|EE017460
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|89761601|gb|DY689546.1|DY689546
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
EST: gi|211160900|gb|FL243906.1|FL243906
EST:     CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAG                         GATGATAAGAAAGACGAAGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG
genomic: CCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTG

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: 718

CGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 470

CGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 494

CGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 444

CGTGCCGGAGAAGGCCGAGCTTGACGACCCTCTCCTGGATGATTTCAAGGCCATCTTCGAGAAGTTCACCTTCAAGGACGCTGCTGCAGCGGCGGCCGAGgtatttggat ... tcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcggtcggtcgattggtgagcccaaactctggtgtcctgatgttcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA
                                    tcctgat  putative branch site (score: 444)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttggattaaccaagtgtttcttcagtcggtcggtcgattggtgagcccaaactctggtgtcctgatgttcgctgacagGATGATAAGAAAGACGAGGGTGCCGCTGATGCCACAAAGAAGGGGTCACTGGATGATGATGACGACGACGAAGATGATGAGCAGGAGGCAAACAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG