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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaactatgaaacatatgtatttatagtattgccacttaaaacaacagggttttcttatttatatgtaacatccaatttgctttttttatgttcag

Basic information

species Zea mays
transcript GRMZM2G113619_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113619_T04 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os09g24650.4 (Oryza sativa), 5'ss of exon 5
ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaacta-------tgaaacatatgtatttatagtattgccacttaaaacaacagg-gttttcttatttat----------atgtaacatccaatttg-----ctttttttatgttcag
 |||||||| ||||| |||||||| |||||||||||||| |||||||| |||||||||||||| ||||||||||| || || |||||||||||||| |||||||||  |||        |  ||| |||||||||||    |     || | |||||||  || ||  |||| ||          ||| ||  ||   |||      ||||  ||||||||||
CCTTGCAGTTGCACAGAACCACATTATGGAAGCTGAATACGATGATTACTCTGCCACAAATGCCAGCACTGCTGCTTTTTGTCGCTCTGCTGCTCTAGTTgtgagttcctaatttctgcgccacaaatgtatttata----tattttttgagacaacagatgtatttatattgattgcacatgtaatggaaggtcttgtttatttacctttgcttatgttcag
















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|6827480|gb|AW331123.1|AW331123
EST:     CTGCC-CAAATGCGAGC-CTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|93283252|gb|EB675516.1|EB675516
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|50326768|gb|CO521894.1|CO521894
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|94472719|gb|EB701677.1|EB701677
EST:     TTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|60337669|gb|DN204642.1|DN204642
EST:     CCACAAATGCGAGCACTGATGCCTTCTGCCGTTTTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|78086641|gb|DV515034.1|DV515034
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|93284055|gb|EB676319.1|EB676319
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|60338944|gb|DN205917.1|DN205917
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|71311804|gb|DR792363.1|DR792363
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|91877838|gb|EB407795.1|EB407795
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|71766652|gb|DR964589.1|DR964589
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
EST: gi|76280759|gb|DV020327.1|DV020327
EST:     CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTT                         TTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT
genomic: CTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGAT

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: 211

ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 158

ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 179

ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaact ... ttatgttcagTTAATGGCTCTCTTATTGTTGAGACACGCACTGACTCTAACTGATGAAGATGACGACGACACTTCAGCGATGTTTTCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTGCAGTGGCACAAAACCACATCATGGAAGCTGAATATGATGATTATTCTGCCACAAATGCGAGCACTGCTGCCTTCTGCCGCTCTGCTGCTCTTGTTgtgagtaactatgaaacatatgtatttatagtattgccacttaaaacaacagggttttcttatttatatgtaacatccaatttgctttttttatgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT