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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacatgctaatctactacactctgttaggatatttttttcctagaaataccagttcgatacattttactcatctactgcctggtgaatggtattgcag

Basic information

species Zea mays
transcript GRMZM2G081622_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081622_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 5'ss of exon 4
TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacatgctaatctactacactctgttaggatatttttttcctagaaataccagttcgatacattttactcatctactgcctggtgaatggtattgcag
|  |||||||||| |||||||| ||||| || |||||||||||||||||||||||||||||||||||||||||||| ||||||| |||||||||  ||||||||| ||| ||||| ||| ||||  | | || | | ||| || |  | |||     |||||| |  || ||     | | |||                   
TTCTGAGCAAGCCTTCTTTGACTGGGATCCCATTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCTAAGCAAAGCTTCACAGACGTAATgtaagtacacgctaagctattacagaccgataaggt-tttcttacgcacaaacctgtgttcgacaagttatatgtgac-attgcag-----------------
















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|32941655|gb|CF046474.1|CF046474
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|116823538|gb|EC867078.1|EC867078
EST:     AAAATTGACAAAGCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|71310462|gb|DR791536.1|DR791536
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|13237001|gb|BG355015.1|BG355015
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|37401762|gb|CF638249.1|CF638249
EST:     GCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: GCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|32870322|gb|CF010004.1|CF010004
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|5296276|gb|AI783046.1|AI783046
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|6865359|gb|AW360709.1|AW360709
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|32941541|gb|CF046360.1|CF046360
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|32794190|gb|CD946426.1|CD946426
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|32870323|gb|CF010005.1|CF010005
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|71434589|gb|DR815639.1|DR815639
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|71310460|gb|DR791535.1|DR791535
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|67015039|gb|CO443788.1|CO443788
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|149086640|gb|EE176182.2|EE176182
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|148949509|gb|EC894973.2|EC894973
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|78105314|gb|DV523732.1|DV523732
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|78022902|gb|DV491289.1|DV491289
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|78081076|gb|DV509488.1|DV509488
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|32851483|gb|CD991164.1|CD991164
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|14203624|gb|BG837301.1|BG837301
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|32862706|gb|CF002388.1|CF002388
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|5762128|gb|AI967176.1|AI967176
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGNCATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|9566365|gb|BE475874.1|BE475874
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|76283087|gb|DV022655.1|DV022655
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
EST: gi|37392828|gb|CF633667.1|CF633667
EST:     AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAAT                         GGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG
genomic: AAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTG

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: 117

TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTGCAAGAACTCTACCAACATTGATTCTGTCATTGAATGGCTGGTGAAGCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTGCAAGAACTCTACCAACATTGATTCTGTCATTGAATGGCTGGTGAAGCAC


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

TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTGCAAGAACTCTACCAACATTGATTCTGTCATTGAATGGCTGGTGAAGCAC


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 103

TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacat ... ggtattgcagGGGCCTAAAGACAATCACTGACCGAGAAGTGGCATGTTTCATGACATCTTGCAAGAACTCTACCAACATTGATTCTGTCATTGAATGGCTGGTGAAGCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGAGCAAGCCATCTTTGACCGGGATTCCGTTACTAGTCATTGGCAATAAAATTGACAAACCTGAAGCTTTCCCCAAGCAAACCTTCACAGAACTAATgtaagaacatgctaatctactacactctgttaggatatttttttcctagaaataccagttcgatacattttactcatctactgcctggtgaatggtattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA